BioStation
BioStationViewer Open Ver.1 Rev.23

Users Manual(Lite version)

2021/7

Contents
1.

Introduction.................................................................................................................... 1

2.

How to use BioStation Viewer ...................................................................................... 2
2.1.

Getting Start BioStation Viewer ........................................................................... 2

2.2.

Explanation of Menu .............................................................................................. 3

2.2.1.

File.................................................................................................................... 3

2.2.2.

Viewpoint ....................................................................................................... 23

2.2.3.

Model .............................................................................................................. 25

2.2.4.

Color ............................................................................................................... 31

2.2.5.

Selection ......................................................................................................... 32

2.2.6.

Tool ................................................................................................................. 33

2.2.7.

Monitor........................................................................................................... 42

2.2.8.

Edit ................................................................................................................. 54

2.2.9.

Preferences .................................................................................................... 54

2.2.10.

Help ............................................................................................................ 60

2.3.

Shortcut panel ...................................................................................................... 61

2.4.

Section ................................................................................................................... 63

2.5.

Trajectory .............................................................................................................. 65

2.5.1.

File format ..................................................................................................... 65

2.5.2.

Control animation ......................................................................................... 66

2.6.

VISCANA .............................................................................................................. 71

2.6.1.

Menu .............................................................................................................. 72

2.6.2.

Data tab ......................................................................................................... 74

2.6.3.

Analysis tab ................................................................................................... 77

2.7.

IFIE MAP .............................................................................................................. 79

2.8.

FILM Isosurface ................................................................................................... 90

2.9.

Basic Action .......................................................................................................... 95

2.9.1.

Enlargement, Shrink, Rotation and Translate ........................................... 95

2.9.2.

Coordinate Rotation and Translation of Molecule Structure .................... 95

2.9.3.

Control of visualization area ........................................................................ 96

2.10.

How to Select Structures as Subjects .............................................................. 97

2.11.

Setting Preference Categories ......................................................................... 98

2.12.

Setting the Bounding box ................................................................................. 99

2.13.

Molda ............................................................................................................... 101

2.13.1.

Creation DNA .......................................................................................... 101i

3.

2.13.2.

Creation RNA .......................................................................................... 104

2.13.3.

Mutation DNA ......................................................................................... 106

2.13.4.

Mutation RNA ......................................................................................... 110

2.13.5.

Adding Nucleotides of DNA .................................................................... 114

2.13.6.

Adding Nucleotides of RNA .................................................................... 130

Examples of How to use ............................................................................................ 136
3.1.

Displaying the Results of ABINIT-MP Calculations. ...................................... 136

3.1.1.

Displaying Molecular Structures ............................................................... 136

3.1.2.

Changing Colors .......................................................................................... 139

3.1.3.

Adding Labels .............................................................................................. 141

3.1.4.

Displaying the Isosurface of the Electron Density ................................... 142

3.1.5.

Adding Colors to the Isosurface of the Electron Density by the Value ofElectrostatic Potentia. ............................................................................................... 143
3.1.6.

Isosurface of Electrostatic Potential .......................................................... 144

3.1.7.

Isosurface of Molecular Orbitals ................................................................ 145

3.1.8.

Electron field vector .................................................................................... 146

3.2.

Example of Structures of Estrogen Receptors – Ligand Complexes .............. 149

3.2.1.

Peptide Chains in the the C Line Model ................................................. 149

3.2.2.

Modifying the model of C Line of Peptide and the model of Ligands ... 150

3.2.3.

Display Peptide Chains in the CLine Model+ Ligands+ Selected Residues
153

3.2.4.

Display Ligands and Charged Residues .................................................... 155

3.2.5.

Display Atoms around Ligand in specified Distance................................ 157

3.3.

Example of the Display of Interaction Energy between Fragments .............. 159

3.3.1.

Load File ...................................................................................................... 159

3.3.2.

Assignment of Interaction Energy between Fragments .......................... 160

3.3.3.

Assignment of Threshold ............................................................................ 161

3.3.4.

Interaction Energy between Selected Fragments..................................... 162

3.4.

How to Overlay ................................................................................................... 163

3.4.1.

Load File ...................................................................................................... 163

3.4.2.

Overlay with All the CCoordinate .......................................................... 164

3.4.3.

Overlay by Atom(C within Selected Residues) ....................................... 164

3.5.

Example of How to Add Hydrogen .................................................................... 167

3.6.

Example of Interfragment interaction energy N:1 .......................................... 169

3.7.

Example of trajectory ......................................................................................... 170

3.7.1.

Glyine ........................................................................................................... 170

ii

3.7.2.

Si8................................................................................................................. 171

3.7.3.

Create a movie file of trajectory ................................................................. 172

3.8.

Example of crystal .............................................................................................. 174

3.8.1.

Load a file and visualize the isosurface ..................................................... 174

3.8.2.

Periodic display ........................................................................................... 175

3.8.3.

Display a section ......................................................................................... 175

3.8.4.

Display bond ................................................................................................ 178

3.9.

Example of CHPI ................................................................................................ 179

3.9.1.

Method for exploring XH/π contacts .......................................................... 179

3.9.2.

Edit parameter ............................................................................................ 180

3.9.3.

Edit PI Information file .............................................................................. 183

3.9.4.

Execute program ......................................................................................... 187

3.10.

Analysis sample of electron density grid data of the CNS form ................. 189

3.10.1.

Example of AJF ....................................................................................... 189

3.10.2.

An display example of grid data of the CNS form ................................ 190

3.10.3.

An example : the extracted electron density around protein is used .. 191

3.10.4.

Compare grid data ................................................................................... 192

4 Super molecule ............................................................................................................... 193
5 Option of optimize structure ......................................................................................... 196
6 Installation ..................................................................................................................... 200
6.1 Distribution.............................................................................................................. 200
6.2 System Installation ................................................................................................. 200
6.3 System Requirements ............................................................................................. 200
6.4 File Acquisition........................................................................................................ 200
6.5 Reduce ...................................................................................................................... 200
6.6 Babel......................................................................................................................... 202
6.7 Bond Builder ............................................................................................................ 203
6.8 TINKER ................................................................................................................... 204
7 Acknowledgement .......................................................................................................... 205
8 References....................................................................................................................... 207

iii

1. Introduction
List of key BioStation Viewer features:
1) Visualize molecular structures of Protein and DNA
2) Visualize isosurface of electron density, electrostatic potential and molecularorbitals.
3) Visualize isosurface of the electron density, added colors by the value of electrostatic
potential.
4) Edit molecular structures5) Visualize the interaction energy between fragments
6) Visualize Electron Field Vector
7) Animate molecular trajectory
Fig1.1 shows an example of isosurface of electron density, added colors by the value ofelectrostatic potential

Fig1.1

Isosurface of Electron Density, Added Colors by the Value of Electrostatic

Potential

1

2.

How to use BioStation Viewer

2.1.

Getting Start BioStation Viewer

Double click on the iconof the desktop to start Viewer. Fig2.1 shows the main

window. Molecular structures are shown on the hierarchical window on the left side of
the window, the viewing-window by a 3-dimensional image (3D) on the middle andshortcut commands panel on the right. You can choose display option from the menubar. The hierarchical window shows a tree-view of the molecule, the layer of molecule bychains, residues and atoms. By selecting an icon in hierarchical item, the appropriate
atom in 3D view-window is highlighted. By selecting the displayed structure in 3D
view-window, the appropriate items in hierarchical window are highlighted.
message appears at the bottom of the window.

Fig2.1 Main Window

2

The

2.2.

Explanation of Menu

Fig2.2 Menu at main window
2.2.1. File

Fig2.3 File menu Open Load PDB file(*.pdb,*.ent) 、 ABINIT-MP Check Point File(*.cpf) 、
ABINIT-MP Grid File(*.den,*esp,*.map,*.mo) 、 MOL2 file(*.mol2) 、 MDL
file(*.mol,*.mdl)

andGaussianCube

file(*.cube,*.cub),

XYZfile(*.xyz),

Trajectory file (*.trj,*.tr2,*.trj2,*tj2), Pno file(*.pno), Display profile（*.prof）.
Please refer to the specification of each file from the following URL.


ABINIT-MP : http://www.fsis.iis.u-tokyo.ac.jp/result/software

PDB File： http://www.rcsb.org/



MOL2File： http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
MDL File：

Gaussian Cube File： http://www.gaussian.com の G98 Manual Pages

XYZ File：Describe number of atom at first line, comment line, and atom
symbol, x,y,z coordinate in one line. As extension, in BioStation Viewer, thevector values of x, y and z is specified behind coordinates, and the vector
display for every atom is possible. Refer to the Arrow of Preference3specification for change of the display attribute of a vector.
Mopac input/output file: Dewar, M.J.S., Thiel, W., J. Am. Chem. Soc., 1977,
99, 4899, 3907

Trajectory File : refer 2.5.1



Pno file : http://www.fsis.iis.u-tokyo.ac.jp/result/software

Display profile : you can reproduce the display state by saving in the fileand reading the file. The corresponding functions are shown bellow.
Include 1 of CPF or PDF. The other structure files are not supported

View Point



Model



Color



Atom,Residue (Model,Color,Label)

Tool(Display * in Distance, Set Rotation Center )Monitor(Distance, Angle, Dihedral Angle, Interaction Energy, IFIE
1:1,N:1Preference1) Molecular Structure file
When PDB file、ABINIT-MP Check Point File、MOL2 file, MDL file, XYZ file,
Gaussian output file and Mopac input/output file are loaded, the molecular
structures are displayed. When number of atom lower than 300, display slyle is
Stick, more than 300 is CA (Line).
2) ABINIT-MP Grid File, Gaussian Cube File
The extension of ABINIT-MP Grid File means as follows :i) den :electron densityii) esp :electrostatic potentialiii) map : map file of electrostatic potential on the isosurface of the electron
density.
iv) mo :molecular orbitalsv) efv :electron field vector

When ABINIT-MP Grid File loaded, specify the isosurface value that you wantto visualize.
In the case of a Gaussian Cube file, select the file type from electron density,
electrostatic potential, and a molecular orbital, and specify covering a value ofthe boundary on a periodic display, and performs the display specification of4each. Periodical grid value is selected “On” for add one a cell at edge of boundary,set “Off” that not add a cell. A dialog box shown in Fig2.4.

Fig2.4Gaussian Cube File3) Specify electron density display option
A dialog box for the electron density and electrostatic potential is shown in
Fig2.5. Specify the value of the isosurface value, the color, the transparency,
bounding box and section. There are the two methods of coloring. One is tospecify a single color and the minimum value and maximum are specified, acolor is specified in the range. The Color Preference Dialog Box is shown in
Fig2.6.
There are two types specify of isosurface value a value or sigma. σis calculated
by following equation. If the value is more than 1, it is treated as 1.
2 1/2

∑𝑁
𝑖=1{𝜌(𝑥𝑖 , 𝑦𝑖 , 𝑧𝑖 ) − 𝜌̅ }σ[ρ] = []𝑁

Clicking on the “Set” button , display section specify dialog. Refer to Shortcut
panel 2.3 to set section option.
This sigma function is currently suspended.

4) Density -> CNS
Convert density file to CNS file.

5

Fig2.5 Isosurface Value Dialog Box

Fig2.6 Color Preference Dialog Box
5) Periodic display of density
When reading a density file (*.den) or a CNS file, it's possible to do theperiodic display which you assigned this data as Unit Cell.
When selected Tool-> Periodic menu on Isosurface Value Dialog, periodic
display dialog is showed.

6

Fig2.7 Periodic Dialog Box
It has two mode.
a) Fit Molecule
Include the molecule structure
x,y,z Margin of eachdirection from molecule structureb) Manual
x,y,z

specify Num, Start, Interval

Num : number of cyclic
Start : index of start position. default is 0.
Interval : default value from file.
6) Specify map file and electrostatic potential
In the case of a map file, specify the ranges of both the value of the isosurface
value and that of electrostatic potential. This dialog box is shown in Fig2.8. As
the value of the default is changed from high to low, the visualize color ischanged from red to white to blue. When you set Min Max( red, blue) using the
button for specifying the range of the value, the display color is changed fromblue to white to red.
In the case of electrostatic potential, specify the value of the isosurface value.
The isosurface value is displayed by the two specified values(±).

7

Fig2.8 Map file and Electrostatic Potential Dialog Box7) Specify display option of Molecular Orbital
In the case of the molecular orbital, the orbital energy graph is displayed. The graphwindow is shown in Figure 2.5.

When you move the mouse on each level, the orbital

number and the energy value are displayed under the graph.

When you click on eachlevel, the orbital number is selected in the Mo No. Here the orbital number can be
input directly. When you click on the Draw button, visualize the isosurface of thespecified value (±).
By clicking on ”＋” and”－“ buttons, the graph is scalable. The line width each levelcan be specified with Line Width. Colors of the isosurface value can be specified in theoptional colors dialog box. In addition, Color(-,+) can be changed into Color(+,-), andthe colors will be reversed whenever they are selected.
In Gaussian Cube file, without the energy value, the graph is displayed starting from
1, in the case of the descriptions of multiple orbitals.

8

Fig2.9 Graph window of Isosurface of Molecular Orbital .
8) Specify display option of electron field vector
When a electron field vector file loaded, a dialog box(Fig2.10) pops up anddisplays an electron field vector by the defaults option. An electric field vector
is displayed on the basis of the point on isosurface. Display option is explained
below.

9

Fig2.10 Electron Field Vector Dialog Box

Map Property

Value of Density Isosurface
Specify the value of density Isosurface

Min Max(blue,red)/ (red,blue)
Specify the range of electrostatic value. As the value of the default ischanged from high to low, the visualize color is changed from red to white
to blue.

When you set Min Max( red, blue) using the button for

specifying the range of the value, the display color is changed from blue
to white to red.
Transparency
Specify the TransparencyBounding Box
Specify to display a bounding box.

Section10

Clicking on the Set button, display the dialog box for a section view.
Refer to Shortcut panel 2.3 to set the section options.
Electric Field Vector Property


ModelSpecify the model (Line/Stick). When the stick model is selected, specify
the radius of stick.

Start Value Threshold(min,max)Specify the start point range of electrostatic value on the isosurface

Number of Step
Specify the number of step. It repeatedly calculates the specified numberof times, and a vector is displayed.



Length(Å)
Specify the length of one step.

Thinned-out ratio (0.0-1.0)
Specify the thinned-out ratio of start point. (value range : 0-1)

 Draw
Display electron field vector.
9) Trajectory file
Animate the molecular structure in time series. Refer to Section 2.5 fordetails.
10) Pno(Pair Natural Orbital) file
Display isosurfaces of Pair Natural Orbital. Specify display option for each pairorbital. Display each relaxation energy, occupation number of Hole orbital andParticle orbital. You can specify display on/off each item. The vector is a arrowfrom Hole grid region to Particle grid region.

All pairs can beselected/unselected by “Select All/Unselect All” Button. When a “Apply” button
is clicked, it's displayed by the specified style.
Fig2.11,Fig2.12.

11

A dialog box shown inFig2.11 Pno(Pair Natural Orbital) Dialog Box

Fig2.12 Hole, Particle,Vector Dialog Box

12 Open CPF
You can specify fragments that are subject to display at open dialog. Only the
specified fragments are displayed. Non-display specified fragments are notdisplayed unless you re-read them. There are four modes.
1) None : It is displayed without any specification.
2) Ignore Fragments : Specify fragment numbers that are not subject todisplay3) Fragments in Distance : Display a fragment within the distance from thespecifier fragment.
4) Ignore Fragments by dimer value(CPF R23) : Do not display fragmentsthat are not have dimer value.

Fig2.13 Open CPF Dialog Box

Fig2.14 Exanple of None.

13

Fig2.15 Example of Ignore Fragments

Fig2.16 Example of Fragments in Distance14

Fig2.17 Example of Ignore Fragments by dimer value(CPF R25)

15

 Open File[difference density]
Some Grid files are loaded and the isosurface of difference is displayed. If you
specified different grid size data file, error occurred. The maximum number offiles is 7. The dialog box is shown in .Fig2.18.

Fig2.18 Difference files Dialog Box
 Open File[difference cpf]
Some Check Point files are loaded and calculate charge and IFIE. The dialog
box is shown in Fig2.19.
Adjust Atom Range : Specify a part of atom/Fragment in file that arecalculated.
Format : Start atom No. – End Atom No. Corresponding atomic number inthis file.
Ex. File2 “10-20 5” atom No.10-20 in file1 correspond to atom No.5-15 in file2.
If no specify atom No., all atoms correspond. If selected “Coddinate”, Display
atom No. in this line file.

Fig2.19 Check Point Files Dialog Box

16 OpenFile[Supermolecule]Specify complex, protein and ligand CPF file. The dialog box is shown in
Fig2.20. The fragment number of the protein in a complex is specified like this
“1-100”. Clicking on the Ok button, read files and display the IFIE value
which applied electronic relaxation by ligand binding at 3D List and MAP.

Fig2.20 Supermolecule Dialog Box

 Open File[IFIE Grid Json]
Load IFIE Grid Json files, and display isosurfaces. Specify number of files at“Number of files” and hitting Return key then file input fields are available.
Hitting “Load” key then load files and display energy items. Hitting “Draw”
key then display isosurfaces.

Fig2.21

IFIE Grid Dialog Box17 Save File
You can output each file by selecting the extensions.
1) pdb, ent Save molecular structures by PDB file format.
Atomic numbers in the saved files are renumbered.
2) gjf Output the input file of Gaussian. Here is an example of file. In thecase of a display of ABINIT-MP Check Point File, charged molecules and spin
multiplicities are calculated as follows.
Charged molecules = the sum of charged molecules (the sum of nuclear
numbers ) – the sum of electron numbers of fragments.
Spin multiplicity = If the first letter of an electronic state is S, show 1,
if it is D, show 2, and if it is T, show 3.
%chk=test.chk#HF/6-31G(d,p) POPT=(MaxCycle=100) SCF=TIGHT
0 1
N 0 x001 y001 z001
C 0 x002 y002 z002
C 0 x003 y003 z003……………
H 0 x071 y071 z071
O 0 x072 y072 z072
H 0 x073 y073 z073
Variables :x001= 0.162000
y001= -0.202000
z001= 0.000000
x002= 1.612000……………
z072= -5.671000
x073= -4.846000
y073= 12.697000
z073= -6.024000
Constants :3) jpg Output the JPEG file.
4) png Output the PNG file.
5) tif Outpur the Tiff file.
6) xyz Output XYZ file. It describes number of atom at first line, and atom
symbol, x,y,z coordinate in one line.
7) prof Output display profile file.

18 Save Renumbered PDB
Save

PDB

File

which

renumberedatom

number.

File

name

is

xxx-renumbered.pdb. Specify output “TER”(end of chain) and chain names.

 Ｅｄｉt ABINIT-MP File
Popup the edit window of ABINIT-MP input file.

Here, you can set theparameters, load and save files. How to edit parameters is explained in Section
エラー! 参照元が見つかりません。.
 Ｅｄｉt Gaussian Input File
Popup the simple edit window of Gaussian input file. Here, you can set theparameters, load and save files.
 Ｅｄｉt cpf2den Input File
Popup the simple edit window of cpf2den input file(Fig2.22). Here, you can set
the parameters, load and save files. If loaded Check point file, set the file nameand the value applied to maximum and the minimum value ±2A is displayed at
the column of Domain computing lattice point. Refer to the "ABINIT-MP user’s
manual" for the details of cpf2den.

19

Fig2.22 cpf2den input file edit window

Mo File(*.mo)Specify YES/NO to output the Molecular Orbital grid file.
Reagion : Specify the fragment number. Ex ：’1,2,8-12’
Level : Specify the level of MO. There are some methods shown below.
・Around HOMO-LUMO ： Ex ’ Homo-5:Lumo+5’・All Orbital：’All’
・All occupied Orbital ：’Occ’
・All un occupied Orbital：’Virtual’・Orbital number ： Ex ’1-10’

Electron Density File(*.den)Specify YES/NO to output the Electron density grid file.

Electrostatic Potential File(+.esp)
Specify YES/NO to output the Electrostatic potential grid file.



Map File(*.map)
Specify YES/NO to output the map file.

Electric Field Vector File(*.efv)
Specify YES/NO to output the Electric Field Vector File.



Pair Natural Orbitals(*.pno)
Specify YES/NO to output the Pair Natural Orbitals file.

20Partial Grid
Specify YES/NO to output the Partial Grid file. NO : calculate allmolecular.
Reagion : Specify the fragment number. Ex. ：’1,2,8-12’

Auto Grid
YES/No : Calculate grid size based on Grid Delta Size and Grid Box
SpaceBoundary how/Hide : Specify display boundary.
Grid Delta Size : Specify a grid size. (Unit is Å)
Grid Box Space ： Calculate grid size from molecular size and Grid Box
Space is shortest distance from box to the molecule of edge. (Unit is Å)
NO : Specify number of x, y and z grid, and coordinate of start and end
point. Dialog is shown bellow.



CNS formatted Electron Dnty(*.cns)
Specify YES/NO to output the CNS file.



Restart from fileSpecify YES/NO to output the restart file.

Base Name
Specify base name for output grid file. if do not specify it, use input filename as base name.

 MoldaExecute Molda. Please refer to the manual of Molda for the useage of Molda.
 Molda(with file)
Execute Molda with loaded structure file.
 Density -> CNS
Convert density file to CNS file.
 File List
When multiple files are loaded, select the file, which you want to display. File21

list dialog box is shown in Fig2.23. In the case of ABINIT-MP Grid File, byclicking on Value button, the dialog boxes as Fig2.5, Fig2.8, Fig2.9 and Fig2.10
are displayed, the display option can be modified.

Fig2.23 File List Close File List
You choose the check box and click on Ok in order to delete the display file on
the Viewer. This dialog box is shown in Fig2.24.

Fig2.24 Select Delete Display File
 ExitExit this application.

22

2.2.2. Viewpoint

Fig2.25 Viewpoint menu
Move a viewpoint to the set-position. Fig2.26 shows a coordinate system.
yxz
Fig2.26 Coordinate system
 Front :See the front side( from plus direction on the z-axis ) Back :See the back side( from minus direction on the z-axis)

 LeftSee the left side( from minus direction on the x-axis):

 Right : Top

See the right side ( from plus direction on the x-axis ): Bottom :See the topside ( from plus direction on the y-axis)
See the downside ( from minus direction on the y-axis)

 Rotate X : Rotate around the X axis
 Rotate Y : Rotate around the Y axis
 Rotate Z : Rotate around the Z axis
 Rotation/Translation/Magnify :Move the viewpoint position. The Dialog is shown in Fig2.27 and display
specification is explained below.

23

Fig2.27 Rotation/Translation/Magnify Dialog Box and file menuFile : Load and save a viewpoint position. The file extension is *.pos.
Open ViewPosition File : Load file.



Save ViewPosition File : Save file.

RotationAxis : Specify axis.

Angle : Specify angle.

Translation


X,Y,Z : Specify rach distance of x,y and z directions.

MagnifyScale : Specify ratio.

 Periodic : Function of periodic display. Only the number specified in X, Y and Z
directions displays the same thing. The dialog box is shown in Fig2.28 and thedisplay specification is explained below.

Fig2.28 Dialog Box of periodic display（example of Gaussian Cube file）

24



File


Reset
Reset display.



Close
Close dialog.



X ,Y, Z
Specify the number of each direction and interval. In case of Gaussian
Cube File you specify three values.



Draw
Display periodically.

2.2.3. Model
Model menu consists two parts (Atom/Structure).

Fig2.29 Model(Atom) menu
Atom menu Off : Disable to display
 Wire frame : Molecule appears as a wire frame model.
 Wire frame(with fragment bound) : Molecule appears as a wire frame model,
with a ball on Catom to show the fragment bound Ball & Stick :Molecule appears as a ball & stick model Stick

Molecule appears as a stick model: Stick(with boundary) :Molecule appears as a stick model with BDA.
 Ball & Wire:

Molecule appears as a ball & wire model

 CPK

Molecule appears as a space filling model Backbone ::Backbone appears as a tube model25 C [line] :Display C atom with a line by a spline interpolation

Fig2.30 Model(Structure) menu

Structrue menu
 Off : Disable to display
 C :Display Catom with a straight line C [line] :Display C atom with a line by a spline interpolation

 C [tube] :Display C atom in the tube model by a spline interpolation.

 Line Ribbon : Display Ribbon(Line) Flat Ribbon : Display Ribbon(Flat)
 Solid Ribbon : Display Ribbon(Solid) Cartoon Ribbon : Display Cartoon
Example of ERE_EST.cpf is shown in Fig2.31-Fig2.37.

26

Fig2.31 Cα

Fig2.32 Cα Line27

Fig2.33 Cα Tube

Fig2.34 Line Ribbon

28

Fig2.35 Flat Ribbon

Fig2.36 Solid Ribbon

29

Fig2.37 Cartoon

1) display type of hidrogen All display all.
 Polar display hydrogens that connected N.
 Non Polar display hydrogens that connected except N.
 No No display.

30

2.2.4. Color
Color menu consists two parts(Atom/Structure). Atom and Structure menu has thesame item. The default value is Atom:Atom, Structure:Structure

Fig2.38 Color menu
 Atom

Set colors by atoms

 Residue
Name Set colors by the residue name, in case of DNA by four kind of colors
ATGC



Hydrophilic/Hydrophobic Set colors by Hydrophilic（Hydrophilic/Hydrophobic/Surface/Hydrophobic()/Surface(）/Hydrophobic()

Set colors by Hydrophilic （）). With the exception of the molecule surface,

Hydrophilic/Hydrophobic are colored.


Function Set colors by functions
Function
Color
PeptideAcidAsp,Glu
Basic
Arg,Lys,His
Neutral
Ser,Thr,Asn,Gln
Aliphatic
Gly,Ala,,Val,Ile,,Leu,,Met
Aromatic
Phe,Tyr,Trp
Thiol-containing
Cys
Imono
Pro
Select Residue Set colors by selected residues, and other residues are white.

 Charged Residue Set colors by the value of charged residues.
(＋: Charge

０ :

－:

)

Set colors by the value of charged molecules.If Check point file isersion.2 , you can choose value HF/MP2. The displayed color is changed from red
to white to blue, according to the changing values of electric charges. When the31electric charge is not specified, set colors by atoms.
 Atom

Displayed color by atom charge.

 B Factor

Displayed color by temperature factor. Specify min/max value.

Fig2.39 B Factor Dialog Box
 Fragment

Displayed color by fragment charge.

 Residue

Displayed color by residue charge.

Fig2.40 Charge Dialog Box
 Fragment Set colors by fragments from the eight colors cyclically as follows.
 Chain Set colors to each chain from the eight colors cyclically as follows.
 File Set colors to each file from the eight colors cyclically as well.
 Structure Displayed color by 2nd Structure(αHelix,βsheet,others).
2.2.5. Selection

Fig2.41 Selection menu

32

Click on the display to choose atoms or residues as subjects.
 AtomChoose atoms as subjects.

 Residue

Choose residues as subjects.

 Fragment

Choose fragments as subjects.

2.2.6. Tool

Fig2.42 Tool menu Display Atom in Distance

You can display atoms within the distance fromselected a atom or a residue. Before this menu is selected, click on atoms as
subjects and specify the distance in the dialog box (Fig2.43). In the From
selected option, choose between Atom and Residue. In the Display List option,
specify the display list of atoms, On or Off. An example of the display list is
shown in Fig2.44. The contents of the atom list can be saved in text format
from the [File] – [Save].

In the Distance option, specify the distance.

33

Fig2.43 Display Atoms in Distance dialog box.

Fig2.44 Atom Lists on Distance Display
 Display Residue in Distance

Display residues within the distance fromselected a atoms, a residue or a fragment. The residue can be displayed when
any of the comprising atoms is within the distance. Before this menu is selected,
click on atoms as subjects and specify the distance in the dialog box (Fig2.45). In
the From selected option, choose Atom, Residue or Fragmnet. In the Display
List option, specify the display list of atoms, On or Off. The contents of theatom list can be saved in text format from the [File] – [Save].
option, specify the distance.

Fig2.45 Display Residues in Distance Dialog Box

34

In the Distance Display Fragment in Distance

Display fragments within the distance fromselected a atoms, a residue or a fragment. The residue can be displayed when
any of the comprising atoms is within the distance. Before this menu is selected,
click on atoms as subjects and specify the distance in the dialog box (Fig2.46
Display Fragment in Distance Dialog Box). In the From selected option, choose
Atom, Residue or Fragmnet. In the Display List option, specify the display listof atoms, On or Off.

The contents of the atom list can be saved in text format

from the [File] – [Save]. In the Distance option, specify the distance.Specify
the display label for the whole residues,fragment and atoms.

Fig2.46 Display Fragment in Distance Dialog Box
 LabelSpecify the display label for the whole residues,fragment and atoms.

This dialog box is shown in Fig2.47.

Fig2.47 Display Label Dialog Box
 Display H Bonds [all]Display all Hydrogen bonds. When they are selected

over again, they are deleted.
 Display H Bonds [intermolecular]

Display Hydrogen bonds between

molecules. When they are selected over again, they are deleted.
 Display Dipole moment HF

The value of Dipole moment of HF of each35

fragmentation is displayed by the arrow. The display option can specified The
Preference dialog(Section 2.2.9). The display disappears when selecting it again.
 Display Dipole moment MP2

The value of Dipole moment of MP2 of eachfragmentation is displayed by the arrow. The display option can specified The
Preference dialog(Section 2.2.9). The display disappears when selecting it again.
 Multi Layer

It is available for CPF version 3 or more. Display style : High

Layer:Stick. Middle Layer:Wire frame, Low Layer: Cα Line.
 Reset Model & Color

Reset the display model and colors to the initialcondition. Clear the assignment of each residue and atom.
 Display Selected Residue

Display a dialog box to select residues which you

want to display. This dialog box is shown in Fig2.48.

When you click on the

Select All button, all the residues are selected. When you click on the UnselectAll button, all the residues are unchecked.

Fig2.48 Display Residue Dialog Box
 Add Hydrogen You can add Hydrogen to molecules in the PDB format. Set
Options, Input File and Output File in the dialog box (Fig2.49)

The PDB filename is set in the Input File and the other PDB file name added _addH is set in
the Input File as the initial display.

After the execution, a dialog box isdisplayed, that ask if you want to switch the displayed file to the result file.
Here, clicking on the Ok button lets the display switch. Refer to Section 6.5to set
Reduce, Section 6.6 to set babel, Section 6.7 to set bond Builder.

36

Fig2.49 Adding Hydrogen Dialog Box

Fig2.50 Confirm to replace Dialog Box
 Hydrogen Capping Mode
Specify hydrogen capping mode.
Terminal: specify N,C edge process.
Histidine : select hydrogen type at HIS.

Fig2.51 Hydrogen Capping Mode Dialog Box
 Optimize Structure
Hydrogen Option file : Specify option file for add hydrogen.
Optimize Option file : Specify option file for optimize. Option detail are37

described at Section 5.
Input File : Specify the input file.

Fig2.52 Optimize Structure Dialog Box
 TINKER
Exectute Tinker program and display result.
Program : Select a program. If you select Other, please input program name attext field.
Options : Specify options for selected program.
Input File : Specify the input file.
Key File : Specify the key file.
After the execution, a dialog box is displayed, that ask if you want to switch thedisplayed file to the result file. Here, clicking on the Ok button lets the display
switch. The Result file name is ABC_program name.pdb if input file name isABC.pdb.

Fig2.53 Tinker Dialog Box
 Overlay Molecule This option allows you to overlay molecules. Fig2.54 shows a
dialog box for overlaying molecules.

38

Fig2.54 Overlaying Molecules Dialog Box
Specify Type, Method, and Fit Number (Residue or Atom).
1) Type
Select a type as a subject to overlay from File, Residue and Atom.
2) Method
Select a method from C, Heavy Atoms and All Atoms.

By selecting this menu

in the case of File or Residue in the Type, specify the atoms as subjects.
3) Fit Number (Residue or Atom)You can specify files as subjects and set the numbers of atoms or residues of thefiles. The numbers can be selected by clicking on the residues and the atoms as
subjects from a molecule structure display or Tree figure. You can also type to
input them. If a number is a serial number, connect the serial numbers with ahyphen, “- “. If it isn’t, type them separated by commas, “ , “.
Example 1 In the case of residues from 1 to 5, type” 1-5 “
Example 2 In the case of residues, 1,2,5, type “1,2,5”.
As the number which you select once can be deleted, use Back Space or Delete inorder to cancel it.
If the number of atoms that you type is higher or lower, the lower number isselected. By clicking on the Ok button, an overlaid branch structure is displayed.
Here, the center of the movement each atomic group is that of the gravity of all
the atoms which are used to overlay. RMSD of the selected atoms is shown amessage area
4) SortSpecify sort for typed in atom numbers.
 Complement Main Chain
Complement main chain. Specify main chain No. that is complemented at Start

39

Residue NO. If you do not specify main chain No., viewer complement
automatically for lock main chain. You can select residue No. by clicking residue
object on Tree. Complement PDB File is used to complement. The result file arestored at start folder as xxx_complement.pdb (xxx is original file name)Fig2.55 Complement main chain Dialog Box
 CHPI Execute CHPI program. Please refer section .
 Set Rotation Center

This allows you to set a rotation center for mouse

operation. The display can be rotated around an axis of selected atoms.
 Set File Rotation Center[center od residue mass] The center of gravity of theatomic coordinate of which selected residue is composed is set as the rotation
center.
 Reset Center

Reset rotation center for mouse operation.

 Set File Rotation Center Set the center of gravity in each file for keyboard
operation.
 Add Text Display 3D text on 3D window. The Dialog is shown in Fig2.56. Loadand save file which specified parameter at File menu.

40

Fig2.56 3D Text dialog
Text Specify text.



Font

Specify font.



Style

Specify Plane, Bold, Italic, Bold Italic



Color

Specify color.

Position(%) Specify position. After display text you can adjust the poison bymouse. Although the position of a mouse is at the lower left of a text, it may
shift a little.



Add Display text. Added to the list under a button. Modification anddeletion is possible by choose list.

Modify Modify display property. Click to the text list, display property ofthis text.

Delete Delete text.

41

2.2.7. Monitor

Fig2.57 Monitor menu Distance

Display a distance between atoms. After selecting a menu, clicking

on two atoms lets the distance display.

In this mode, a color of the menu isgreen. By clicking on the same atoms, they disappear on the screen.
 AngleDisplay angles between atoms. After selecting a menu, clicking on

three atoms lets the angles display. In this mode, a color of the menu is green.
By clicking on the same atoms, they disappear on the screen.
 Dihedral Angle

Display a dihedral angle among atoms. After selecting amenu, clicking on four atoms lets the dihedral angle display. In this mode, acolor of the menu is green. By clicking on the same atoms, they disappear on
the screen.
 Interaction Energy

Display the values of the interaction energy between

selected fragments. After selecting a menu, clicking on two atoms lets thevalue of the interaction energy between the fragments display. In this mode, acolor of the menu is green.
 Reset This option allows you to reset an specified monitor.
 VISCANA Amari et al. have proposed the visualized cluster analysis ofprotein-ligand interaction (VISCANA) for virtual ligand screening based on the
FMO method, by using the dissimilarity between the interaction energy

42patterns of two ligands and by representing each data point with a color thatquantitatively and qualitatively reflects the interaction energy. Details aredescribed in Section2.6 .
 IFIE MAP
Two-dimensional visual representation of IEIE matrix . Details are described in
Section 2.7 .
 FILM Isosurface Ishikawa et al. have developed a method named ”fragmentinteraction analysis based on local MP2 (FILM)” by combining the FMO method
and local MP2 (LMP2). This function display isosurface by result of FILE.
Details are described in Section2.8 .
 Compare Density Files Display difference of some CNS files.
 Charge List(HF,MP2,HF NBO,MP2 NBO,HF ESP, MP2 ESP)
Display charge value of HF,MP2,HF NBO,MP2 NBO,HF ESP, MP2 ESP.
It’s also possible to output a list from File menu to a text file.
MP2 is available after CPF Version 2, NBO is available after CPF Version 3.

Atom Display charge list of atoms.

Fragment Display charge list of fragments.



Residue Display charge list of residues.

Residue (DNA) Display charge list of residues. The sum total of the portion
with the as other portion of DNA as a base is displayed.

Example is shown in Fig2.58. It is also possible to output the list to the file.

43

(1) Atom(2) Fragment(3) Residue(4) Residue(DNA)Fig2.58 Example of charge list.


Sum of Charge

The total of the charge of the fragments, residues andatoms within the specified range are displayed. Fig2.59 shows the range
specify window.

44

Fig2.59 The range specify window.

 Interfragment Interaction

1:1
You can set colors by the value of the interaction energy between
fragments. Select a reference fragment before selecting this menu. Set
colors by the energy value from the reference fragment. Selecting thismenu lets a dialog (Fig2.60) display to specify the value type, the range ofvalues and the threshold values to set colors. The selection item of Valuechanges by Version of CPF. Please refer to section 2.7 for details. This isshown by kcal/ mol. Minimum and maximum values of whole files mean
the defaults.
Many Body Calculation (Value:main+side chain)This option is available after CPF Version3. If checked it and the fragment
is divided by fragmentation with a main chain and an another side chain,
the IFIE value is colored one residue from the value which add value ofmain and side one.
Color
Once you modify them, the interaction energy added colors within therange remains displayed until you select this menu next time. When theminimum and the maximum are modified, put 0 to each value in order toset back to the default values. When the threshold value is specified, thefragment under the threshold value of an absolute value can not be
displayed.

This makes it possible to constrain the display on small

fragments of the interaction.
In the case of the selection of this menu, when you click on molecular45

structures, they are added colors by fragments you click.
When the fragments are not selected before opening this menu,
molecular structures are added colors by fragments you select next.

Fig2.60 1:1 Interaction Energy between Fragments Dialog Box

1:1 [lock]Set colors by the value of interaction energy between fragments. Unlike
the description above, when molecular structures are clicked, the reference
fragment is not modified, and the atom’s information which you click on isdisplayed in the message area. Use this in order to get the atom’s
information which you want to focus attention on, leaving the display on thescreen. In the case of this mode, residues and atoms can not be selected
and the display attribute can not be modified.



N:1
Select reference fragments before selecting this menu. Set colors by theenergy value from the reference fragments. Selecting this menu lets a
dialog (Fig2.61) display to specify the base fragments, the range of values
and the threshold values to set colors. User can select multi-fragments on
3D window by pushing the shift key, and also select them on thehierarchical window and the keyboard input.

46

Fig2.61 N:1 Interaction Energy between Fragments Dialog Box



1:N Mapping
Sum of product which is the value of IFIE with the reference fragment, it
is a function to display the color according to the value. The dialog is shownby Fig2.62. There are 4 ways to specify the reference fragment.
1） AllAll Fragments.
2） Fragments
Selected Fragments.
3） Within
The fragments in the specified distance from a fragment.
4） Has Dimer-ES Value
The fragments have the value of PIEDA other than ES is 0.

47

Fig2.62 1:N Mapping Dialog Box
When “Ratio (A/B)” is selected “on”, fragment color with the ratio of the sumof product of a specified target. The range of coloring will be set
automatically 0.0-0.5 0.5-1.0. A is specified at “Target Fragment(A)” and B
is specified at “Base Fragment(B)”. If the denominator and the numerator
have different signs, the value is set 0 when the numerator is positive andthe value is set 1 when the denominator is negative. To classify thefragment to which the value was changed by select On/Off at“Coloring(gray):out of range”. The fragment is painted by gray.

48

Example of gly10 is shown below. Gly1 is set to 1 and Gly8,9 is set to 0.

Coloring(gray):out of range : OFFON

Fig2.63 Example of ratio on 1:N Mapping

N:N
By selecting reference fragments and object fragments, calculate theinterfragment interaction energy between both fragments. Display thevalue on the message area. A dialog box for N:N interfragment interaction
is shown Fig2.64. Before selecting fragments , mark the check box on theleft side of input field.
You can specify which fragments to exclude with or without a covalent bond.
By click ”Covalent bonds”, then covalent bonds display format A-B. It is
editable. Exclusion fragments is chosen at ”Except Fragments” A, B or
Both.

49

Fig2.64 N:N Interaction Energy between Fragments Dialog Box
Example is shown at bellow. Covalent bonds” None, Except Fragments：A,B and Both.

Fig2.65 Example N:N Interaction Energy



List
List the values of the interaction energy between a selected fragment andeach fragment.

This list can be saved in the file.

Select [File]-[Save]

under the menu bar and specify a file name so as to save the file. If thefragment is a side chain, “_s” is added to the residue name. An example ofthe display is shown in Fig2.66.
If PIEDA selected, total, ES, EX, CT+mix, DI, Solvent are displayed.

50

Fig2.66 List of Interaction Energy between Fragments

3 Body List Display value of 3 body and fragment#. If you click a list,
correspond fragment is highlighted. Display options are energy lebel,
maximum value and minimum. An example is shown in Fig2.67.

Fig2.67 Example of 3 body value list.



4 Body List Display value of 4 body and fragment#. If you click a list,
correspond fragment is highlighted. Display options are energy lebel,
maximum value and minimum. An example is shown in Fig2.68.

51

Fig2.68 Example of 4 body value list.

This is example of Fragment Value:main+side chain parameter. The molecule is
Tripcage. This fragments generated separately main chain and side chain. In Fig2.69
SER20 is colored by each value, then In Fig2.70 colored by a residue.

52

Fig2.69 Example IFIE : Colored by fragment

Fig2.70 Example IFIE : Colored by residue

532.2.8. Edit
 Cut (selected)

This option allows you to cut the selected objects.

 Cut(unselected)

This option allows you to cut the unselected objects.

 UndoThis option allows you to undo and cut the objects.

 RedoThis option allows you to redo the previous action.

Fig2.71 Edit menu
2.2.9. Preferences

Fig2.72 Preference menu Set Preferences Popup a preference dialog box, which is shown in Fig2.73. A
specification item is changed with a tab. The value on the right side of the input
field shows the suggested range. If you increase the resolution to make thenice visualization, but you’ll need lots of time and a large memory to display.
When done, click on the Apply button.

Fig2.73 Preference Dialog Box

541) File
This option allows you to load and save files by selecting [Open]-[Save] under
the file menu.

When you execute BioStationViewer, load the file

named .bioViewer from the current directory to the home directory in order.
If there is a file, the setting is reflected.
The value of a default is set with Set Default Value.
2) Rotation① SpeedSpecify the rotation speed when Rotation in the ＶｉｅｗＰｏｉｎｔ is

selected.
3) Projection
Specify Perspective or Parallel for the projection. If user choose Parallel, user
do not magnify/shrink on mouse operation. User do magnify/shrink on
Rotation/Translation/Magnify at the Viewpoint menu
4) Connect Aom
Select judgment standard for connecting bond from Van der Waals or covalent.
Scale factor effect on judgment standard.
5) Resolution① Line Width :Specify a line width of a wire frame model.

② C Line With :Specify a line width of a C[Line] model.

③ Ball :Specify a resolution of a ball and stick model.

④ Stick :Specify a resolution of a stick model.

⑤ CPK :

Specify a resolution of a space –filling model.

⑥ Tube :Specify a resolution of a C[tube] model.

⑦ Ribbon Width ：Specify a width of Ribbon.

⑧ Ribbon Height ：Specify a height of Ribbon(Solid)⑨ Ribbon Line Width ：Specify a width of line Ribbon(Line)⑩ Cartoon α Head Height ：Specify a height of cone of Cartoon(α Helix)⑪ Cartoon α Radius ： Specify a radius of Cartoon(α Helix)⑫ Cartoon width ： Specify a width of Cartoon(other)⑬ Cartoon β Height ：Specify a height of Cartoon(β sheet)6) Radius① Ball :Specify a size of a ball in the ball and stick model.

② Bond :Specify a line width of a bond in the ball and stick model.

③ Stick:

Specify a line width in the stick model.

④ Tube :Specify a line width of Tube in the C[tube] model.

557) Color① Background② Atom :: Select background colors in the display.
Set colors to each atoms. This dialog box is shown in

Fig2.74.

Fig2.74 Atom Colors Preference③ Residue:

Set displayed colors to each residue. This dialog box isshown in Fig2.75.

Fig2.75 Display Colors of Residues Preference56

④ Fragment :Select displayed colors of fragments. This dialog box isshown in Fig2.76. Set colors to fragments, chains and files from theeight colors cyclically.

Fig2.76 Display Colors of Fragments Preference⑤ Chain :⑥ File:Set displayed colors of chains.
Set displayed colors of files.

⑦ DNA : Set displayed colors of ATGC of DNA.

Fig2.77 Display Colors of the DNA⑧ Isosurface:

Set colors of the isosurface value.

This dialog box isshown in Fig2.77.

Fig2.78 Display Colors of the Isosurface Value

57

⑨ 2nd Structure : Second Structure.

Fig2.79 Display Colors of the 2nd Structure⑩ Selected : Set color of selected item.
⑪ IFIE : IFIE value

Fig2.80 Display Colors of the IFIE Value
8) Arrow：Specify the vector property. The dialog box is shown in Fig2.81.
Arrow(Trajectory) : Specify arrow preference for trajectory.
Arrow(Dipole moment HF) : Specify arrow preference for Dipole moment(HF)
Arrow(Dipole moment MP2) : Specify arrow preference for

Dipolemoment(MP2)① Display The On/Off of a display of an arrow is specified.
② Style Specify style of arrow.
1.

Radius Specify the body and head width.

2.

Head Length

3.

Scale

③ Color1.

Specify the head length fix or ratio.

Specify scale of arrow. The length of 1 of a display is 1Å.

Specify color.

Value

Specify min,max value. The display color is changed fromblue to read.
2.

One color Display the color which is specified58

Fig2.81 Arrow Dialog Box9) Number of decimal
Number of decimal for angle, distance, and IFIE value on 3D.

Fig2.82 Number of decimal Dialog Box
10) CHPI
Specify CHPI result preference. The dialog box is shown in Fig2.83.
①

Model Select Model (Line Solid/Line Dash/Stick)②

Color Specify color.

③

Line Width

Specify line width④

Stick RadiusSpecify Stick radius

Fig2.83 CHPI Dialog Box

5911) Multi Layer
Specify the color of each layer. The dialog box is shown in Fig2.84.
① High Layer Color

Specify the color of High Layer② Middle Layer Color Specify the color of Middle Layer

Fig2.84 Multi Layer Dialog Box

12) Font size

Fig2.85 Font size Dialog Box

 Display Commands Specify the presence of shortcut commands panel.
 Display Axis Specify the presence of a coordinate axis in the lower-left side of
the screen.
 Display Direction Specify the presence of the direction to each file by typing.
2.2.10. Help
 View Help(Japanese/English)

Open a Pdf file to display a manual.

60

2.3.

Shortcut panela. File1) Open：[File]->[Open]
2) Close：[File]->[Close]b. Selection3) Atom: [Selection]->[Atom]
4) Residue : [Selection]->[Residue]
5) Fragment : [Selection]->[Fragment]c. Tool
6) Set Center : set center by selected residue.
7) Target View(Residue/Fragment) : Display residues/fragments in 4.5Å from selected
residue.
Model : Stick, Color:selected color on viewer.
right button clicked : display residues/fragments
left button clicked : display dialog.
8) Reset View : reset 3D view state.
9) CHPI : [Tool]->[CHPI]
d. Monitor
10) VISCANA : [Monitor]->[VISCANA]
11) IFIE : display IFIE dialog
12) PIEDA List : display PIEDA List
examples61

e. Preference13) Background: switch background color.

14) Font+ : enlarge the font size(+2)15) Font－: small the font size(-2)16) Resolution＋ : [Preferences]->[Set Preferences] 2 times17) Resolution－ :1/2times18) Axis On/Off：[Preferences]->[Display Axis] ON/OFF

62

2.4.

SectionSection specification is performed on GUI by the specification of the central point, thespecification of a rotation angle, or the normal vector of a section plane. Fringe andisoline are available. It is colored with the value of the file to input. The color scale
range can be manually set to a specific minimum and maximum value. Multi-section isavailable. The diagram of section is shown in Fig2.86, and The Section dialog is shownin Fig2.87.
No.
The number of the specified section is shown. By clicking Add button, add section.
The specified section display as white transparency plane in 3d window. By
clicking Delete button, delete the section.

Specify Section Plane

CenterSpecify the center points(X,Y,Z) of section by using the slider or the keyboard
input.


Angle

Specify the angle of section by using the slider or[x, y, z]

the normal vector of section. A purple axis is thecenter of an angle and an orange axis the is centerof B angle. C rotates centering of the normal
vector of section.

(X,Y,Z)A

When specifying the normal vector(x,y,z),Cmove the section by hitting Return key.
Set Plane

Select a standard plane(xy, yz or xz).

B
Fig2.86 The diagram of sectionSection Property

Display

Specify enable/disable to display the section.


Value

Select value from the electrostatic potential or the electron density.
Color Range

Specify the color range of value.
Type

Select type from fringe or isoline.

63Transparency

Specify transparency.
Number of Lines

Specify the number of Lines . In the case of molecular orbital 1e-8 is zero value.


Draw

Draw the section.

Fig2.87 The Section Dialog box

64

2.5.

Trajectory

2.5.1. File format
The file format are two types.
1) A file extension is trj. The file includes the value of the energy of each step. Type thenumber of atoms at the first line, an energy value at the next line and the coordinate
of atom. Without energy value, type 0 at the energy line. # is a comment until theend of the line.
Add Fragment No. at end of line for recognition of fragment. There may not be thedescription by you if there is no necessity of the fragmentation. Before load fileselect Color -> Fragment, molecular structure is colored by fragment number.
Example of file.
1000# number of atom
# step 09.87654 # energy
O 1.23345678 1.23345678 1.23345678
H 1.23345678 1.23345678 1.23345678
N 1.23345678 1.23345678 1.23345678
C 1.23345678 1.23345678 1.23345678.....
# step 1
9.87654 # energy
O 1.23345678 1.23345678 1.23345678
H 1.23345678 1.23345678 1.23345678
N 1.23345678 1.23345678 1.23345678
C 1.23345678 1.23345678 1.23345678.....
Example of file with fragment number
1000# number of atom
# step 09.87654 # energy
O 1.23345678 1.23345678 1.23345678 1
H 1.23345678 1.23345678 1.23345678 1
N 1.23345678 1.23345678 1.23345678 1
C 1.23345678 1.23345678 1.23345678 2.....
# step 1
9.87654 # energy
O 1.23345678 1.23345678 1.23345678 1
H 1.23345678 1.23345678 1.23345678 1
N 1.23345678 1.23345678 1.23345678 2
C 1.23345678 1.23345678 1.23345678 2
.....

65

2) New trajectory file format. File extensions are trj2, tj2,tr2. It is extensional format
of XYZ. The number of atoms, a comment, atomic coordinates, and the vector
value are described for every step. A comment is expressed in the group of a tag
and a value and displays graph with this value. When a tag is “Label”, it becomes
the text of 3d viewer. "=" is described between a tag and a value. There may be ","between items. Refer to the Arrow of Preference specification for change of thedisplay attribute of a vector.
Example of file.
8label="MDstep
1"
Ekin(Ha)=0.0000000000
Epot(Ha)=-31.6395526318
Etot(Ha)=-31.6395526318 Fmax(Ha/bohr)=0.1505408174
Si 0.8686973703168 0.5700826492704 0.67866982056 -0.090561 0.076468 -0.082145
Si 4.6421015726304 4.7235419510976 4.75068874392 0.026857 0.018088 0.002683
Si 0.67866982056 3.4204958956224 3.5019362740896 -0.022970 0.000783 -0.024173
Si 4.75068874392 2.03600946168 2.03600946168 0.032733 -0.001620 -0.002599
Si 3.4204958956224 0.7872569918496 3.3933491028 -0.012222 -0.029104 -0.017059
Si 1.764541533456 4.886422708032 2.03600946168 0.101043 -0.077951 0.079853
Si 3.5019362740896 3.3933491028 0.7058166133824 -0.050445 -0.000565 0.003814
Si 2.03600946168 2.0088626688576 4.6421015726304 0.015567 0.013899 0.039625
8label="MDstep
2"
Ekin(Ha)=0.0000001274
Epot(Ha)=-31.6395536508
Etot(Ha)=-31.6395535234 Fmax(Ha/bohr)=0.1505348131
Si 0.868696441081553 0.570083434040259 0.678668977580644 -0.090558 0.076465 -0.082141
Si 4.64210184833175 4.72354213683881 4.75068877143722 0.026857 0.018087 0.002683
Si 0.678669585076125 3.42049590356006 3.50193602590547 -0.022970 0.000783 -0.024173
Si 4.75068907994755 2.0360094452755 2.03600943522114 0.032732 -0.001620 -0.002599
Si 3.42049577020739 0.787256693393632 3.39334892764233 -0.012222 -0.029103 -0.017058
Si 1.76454257011423 4.88642190844518 2.03601028084638 0.101040 -0.077948 0.079849
Si 3.50193575655425 3.39334909697905 0.705816652541516 -0.050443 -0.000565 0.003814
Si 2.03600962149153 2.00886281120628 4.64210197903853 0.015567 0.013899 0.039623…..

2.5.2. Control animation
Load a trajectory file from File menu at the main window. Display processing is
performed at the time of file reading. In proportion to the number of steps, the numberof atoms, and the display style of molecular structures, it takes processing time. After
processing pop up a trajectory control dialog box(). If the file includes energy, an energy
graph appears on the panel.

66

Fig2.88 Trajectory Control Dialog box1) menu

File Create image files
Output a JPEG file to create an animation file at the specified directory. The
file name is imageXXX.jpg. Sequential numbers go into XXX. Specify Output
Folder and Screen Size, and by clicking Create button, display each step andoutput files. However, keep in mind that it may drop out some frames with theperformance of CPU and a graphic card.

67

Fig2.89 Create Image Dialog box

 Create Video File
Create video file as output file name. You can choose two Video Format,
MSVIDEO and Quick Time. MSVIDEO needs a large disk but easy to use with
Power Point. Quick Time file is small file size and needs Quick Time player toplay video.

Fig2.90 Create Video Dialog box

 Save Graph Image File
The graph currently displayed can be saved as JPEG, PNG, or a Postscript file.
Form is judged by the extension of the file name specified on the file selection
dialog.
 CloseClose this dialog.

68



Mode
 Cyclic
Play cyclic.



TextSpecify 3D text property. Font, Style, Size, Color and Position. The dialog box isshown in Fig2.91.

Fig2.91 Text Dialog boxWidth AjustThe size of a graph horizontal axis is united with the size of a display window,
and the whole is displayed.

2) Control Panel

topskip to the top frame.

reversereverse playbackback 1 frame



stop
stop



tail
skip to the last frame

69



play
play



forwardforward 1 stepInterval Time [sec]Interval Time. Too small value is not available.



Current Step No.
Display a current step number. If user input a step number and hit Return key,
display that frame. The step number starts from 0.

70

2.6.

VISCANA

The visualized cluster analysis of protein-ligand interaction (VISCANA) for virtual
ligand screening based on the FMO method, by using the dissimilarity between theinteraction energy patterns of two ligands and by representing each data point with acolor that quantitatively and qualitatively reflects the interaction energy.
When you select [Monitor]-[VISCANA], popup an window of VISCANA(Fig2.92).
Main View consists three parts. At the left side, show the dendrogram that described
result of cluster analysis. At the middle part, show the ligand name and add color bybinding energy. When you take the mouse cursor on the item, show the binding energyof this ligand. At the right side, show interaction energy between ligand and eachfragment of protein.
When you take the mouse cursor on the item, show the interaction energy andfragment number. It is working with 3D View. Select a fragment by push left button ofmouse cursor on the fragment, and clicked “3D Model View” button, display molecular
structure on 3D View with highlighted that fragment. It is easily understood where
there is a position of the fragment that you are selected.(Fig2.93)
There are two tabs ”Data” and ”Analysis” the lower part of window. Specify display
properties at “Data” tab, display result of Cluster Analysis at “Analysis” tab.

Fig2.92

VISCANA window71Select 2GIUcell, and click “3D Model View” button

Fig2.932.6.1.

Menu



File menuHigh light No.40 fragment.

 Load CSV File
Load CSV file and visualized. File format : 1 line shows 1 file.
file name, value#1, value#2 …. value#N
It continues number of files.
 Save image
Save image file(PNG/Tiff)
 Save CSV file(Raw data)72

Output IFIE raw data as CSV.
"1ERE H2O EST600","0.06704805904155364","0.004935882592690177","-0.004161305550951511","-0.003949102"1L2J ETC600","0.09012984097353183","-0.01233636905089952","-0.06828176585258916","-0.01509068469749"2I0G I0G1","0.017258612366276793","-0.001573896166519262","0.018046159180812538","0.007235390599817"1QKM GEN600","0.06880561851721723","-0.021663096427801065","0.014909053323208354","0.00948922598036"1U3Q 272501","0.03297848604415776","-0.022831991052953526","-0.029928279720479622","-0.030791792451

Fig2.94

Example file of Save CSV file(Raw data).

 Save CSV file (Raw data with cluster#)
Output IFIE raw data with cluster# as CSV. Cluster# is specified at Analysis
TAB.

"Cluster","Title","GLU266(1)","GLN267(2)","LEU268(3)","VAL269(4)","LEU270(5)","THR271 …
"1","1L2J","0.004422543410328217","-0.0017177658883156255","-0.00244106788886711","-0 …
…
"1","2YJD","0.0018548246443970129","-0.016161552906851284","-0.01687829554430209","-0 …
"2","1QKM","-0.01033311647188384","0.016623245552182198","-0.009609946864657104","-0.

…

…
"2","1X76","-0.0112376005272381","-0.0026311323599657044","-0.021413976384792477","-0 …
"2","1X78","0.007286158637725748","0.010399236518424004","-0.010982639651047066","-0.

…

"2","1X7B","-0.028911706773214974","0.002566304348874837","-0.011377972521586344","7.

…

"3","1U3R","-0.029407480076770298","0.007906074039055966","-0.0059105008986080065","0 …
"3","1ZAF","-0.027610782271949574","0.009124418895225972","2.941601269412786E-4","0.0 …
"3","2QTU","0.023051065276376903","0.011827122478280216","-0.0036844993592239916","-0 …
"3","2NV7","-0.04559103159408551","0.010739662931882776","-0.0036646668886533007","0.

…

"4","2Z4B","0.023356488600256853","0.008737203490454704","-0.0036989772343076766","-0 …
"5","2GIU","0.04086011557956226","-0.008129799374728464","-0.018197902871179394","-0.

…

"5","3OMO","0.00813774490961805","-0.010438287048600614","-0.01630014342663344","-0.0 …
"5","3OMQ","-0.01761319577053655","-0.013049710614723153","-0.021847352050826885","-0 …
"5","3OMP","0.05095229222206399","-0.0370117163984105","-0.022769159768358804","-0.03 …

Fig2.95 Example file of Save CSV file(Raw data with cluster#).

73 Save CSV file (filtered data)
Output IFIE data from Base Fragment in specified distance. Specify output file
name(ex.

IFIE_filtered.csv),

thenoutputindex

information

file(ex.

IFIE_filtered_fragment_number.csv) . Example shows in Fig2.96.
"1ERE H2O EST600","0.06704805904155364","0.004935882592690177","-0.004161305550951511","-0.003949102"1L2J ETC600","0.09012984097353183","-0.01233636905089952","-0.06828176585258916","-0.01509068469749"2I0G I0G1","0.017258612366276793","-0.001573896166519262","0.018046159180812538","0.007235390599817"1QKM GEN600","0.06880561851721723","-0.021663096427801065","0.014909053323208354","0.00948922598036"1U3Q 272501","0.03297848604415776","-0.022831991052953526","-0.029928279720479622","-0.030791792451
a)output file

"1ERE H2O EST600","1;19;19","1;20;20","1;21;21","1;33;33","1;34;34","1;35;35","1;36;36","1;37;37","1"1L2J ETC600","2;19;17","2;20;18","2;21;19","2;33;30","2;34;31","2;35;32","2;36;33","2;37;34","2;38;
2I0G I0G1","5;19;17","5;20;18","5;21;19","5;33;30","5;34;31","5;35;32","5;36;33","5;37;34","5;38;35""1QKM GEN600","3;19;17","3;20;18","3;21;19","3;33;30","3;34;31","3;35;32","3;36;33","3;37;34","3;38;"1U3Q 272501","4;19;17","4;20;18","4;21;19","4;33;30","4;34;31","4;35;32","4;36;33","4;37;34","4;38;b)index information

Fig2.96 Example file of Save CSV file(filtered data).
 CloseClose this window.
2.6.2.
1)

Data tab

CPF Data DirectorySpecify data directory that stored data files. The result files are check point files
that applied to different ligands for the same protein and must be same fragment
number. Click “Load” button then load files. After load files, “3D Model View”, “Apply”
button and “Ligand Fragment No.” is available.

2)

Data SelectSpecify energy type for clustering. IFIE Energy or PIEDA value.

Fig2.97

Data Select Panel.

74Fig2.98 Example of Legend.

3)

Cluster Analysis

Fig2.99 Cluster Analysis Panel.
Base Fragment
It is base fragment number that for cluster analysis.

IFIE/PIEDA(X)
Specify color and range of Interaction Energy. The default min/max value set
from loaded file.

Sum over X
Specify range of Binding Energy. The default min/max value set from loaded file.

Cluster Method
Select method for cluster analysis. There are bellow methods.
 furthest neighbor nearest neighbor group average centroid
 median Ward flexible



Apply
Click “Apply” button, then redisplay by specified parameter.

4)

View Filter75Distance
Specify distance from Base Fragment.

Distance TypeSpecify distance method.
Neaest Interatomic : nearest distance between atoms.
Center of mass :distance from center of the fragment.

FilterClick “Filter” button, then redisplay by specified parameter.

Fig2.100 View Filer Panel.
5)

3D Model View
” 3D Model View” button function : At first visualized data and select a fragment on

the right side, then click ” 3D Model View” button, display molecular structure on 3D
View with highlighted fragment. Show the example (エラー! 参照元が見つかりません。) .

76

2.6.3.

Analysis tab

Display yellow dash line on dendrogram at mouse position, when select “On” at“cluster No” parameter. Then display cluster# root of dendrogram. When you’d like todisplay the cluster # in the desired position, hold the mouse cursor in that position andit goes out of the top or the bottom of dendrogram.

Fig2.101 Analysis tab.
When a horizontal line of a dendrogram is clicked, the selected cluster number is shownas "*", and ligand name set on the text area at checked box #1 or #2. Color of ligandname #1 set magenta and #2 set green. If you click other than a horizontal line, theselection will be canceled.

Fig2.102

Select cluster.

77

Click “Apply” button then calculate the difference of average in values. Display
fragment number and value in order absolute value on the Result list panel. If clicked
list value, the applicable fragments are displayed in a yellow frame.

Fig2.103 Example of cluster analysis.

78

2.7.

IFIE MAP

The IFIEs illustrate the information about the interaction energies between the
fragments consisting of amino acids, nucleotides and other molecules. The whole IFIEs
are represented as a matrix form called an IFIE matrix and visualized as MAP. The
Map add color by IFIE value, and Second Structure is shown at upper and left part. By
clicking on “＋” “－“ buttons, the graph is scalable. When you take the mouse cursor on
the item, show the interaction energy and fragment number. By clicking the item,
display highlighted that fragments on 3D View.
Select File->Open File menu and load check point file. Select Monitor->IFIE MAP
menu then IFIE window is displayed. Example is shown in Fig2.104

Fig2.104

IFIE MAP Window

1) Instruction of menuFile menu Save image
Save image file(PNG/Tiff/Jpeg).
 Save text

79

Save text file(index, value).
 CloseClose this window.
2) Visualize Parameters
A specification item is changed with a tab. When "Apply" button is clicked after
parameter specifies , the MAP is changed.


Display Value
The color parameter panel is shown in Fig2.105.

Fig2.105

IFIE MAP Display Value panel

80 Format

Fig2.106Format panel

Separate(-/+)
The negative values are displayed on left side and the positive values
are displayed on right side. The example is shown in Fig2.104.

Symmetric
The negative/positive values are displayed on both side. The example
is shown in Fig2.107.

Distance Matrix
The Symmetric is displayed on left side, the distance between
fragments is displayed on right side. The atom that becomes base of
distance is specified next panel. The example is shown in Fig2.108.

Fig2.107 Example of Symmetric81

Fig2.108



Example of Distance Matrix

Value
Select the kind of energy. This menu item changes by the version of CPF. The
each menu item is shown in Fig2.109.

a) Version1b) Version282c) Version3,4.-4.2, 7.0d) Version 4,201, 7.0-4.0, Open1.0 rev10e) Open1.0 rev21 では、記述されていないエネルギーはグレーアウトされる
Fig2.109

IFIE MAP Value panel each version

In case of the result of super molecule, Super Molecule Step2 button is available,
select this button and the step2 result is displayed as MAP.
In case of the result of many body, Many Body Correction button is available, selectthis button and the many body correction value is displayed as MAP.
If CPF version is 3, you can choose compound-IFIE. This dialog is shown in Fig2.110.
Calculate value from some results. Specify coefficient and Value for each file.

83Fig2.110

Compound IFIE Dialog box

Color AutoAdd color by range of value(min,max) each of Color(-) and Color(+). Log
and linear can be specified for the type of scale. If 0 is specified as Ｌｏｇ
value, it is changed to 1e-10.
If you select ”Colored” as Outside the range, the beyond the limits ofminimum/maxmum value is displayed by the color of the maximum
value and minimum value. If you selects ”None”, do not add color.
 CustomThe value within specified range (min<max) is displayed by the specified
color. It becomes white outside the range. When "Color" button is clicked
popup the color dialog. The example is shown in Fig2.111.

84

Fig2.111 Example of custom colorDistance Matrix
Add color by range of value(min,max). Log and linear can be specified forthe type of scale. If 0 is specified as Log value, it is changed to 1e-10.

Distance Matrix(Base atom)
Specify the atom that becomes base of distance incase of peptide, DNA andothers.
1) Center of Mass
2) The shortest interatomic
3) custom
Please specify atom type name in the check point file. In the case ofDNA(1fragment is 1DNA) , select as the base atom either of backbone or base. In
the case of others(fragments is not peptide and DNA), specify the base atom intext field. This format is “fragment No. : atom name”. If there are someparameters, input parameters that are separated by the space character.
Example “222:C3’ 244:P”

85

Fig2.112
Distance Matrix 表示例

Fragment Order
Specify the order of displaying the fragmentation on MAP.
All: specify the order for all fragments.
Chain : specify the order for each chain.
If mark the check box , it is displayed. It is displayed in input order and theformat is possible to specify it as follows.
1) Start fragment No. ― End fragment No. ： increment
Specify the start fragment No. , end fragment No. and increment.
example 200-220:2
2) Residue name
It is specified three character such as GLY, ASP.
(This format is only available in All)

Clear fragments
Clear input parameters.



Set Default
Set default values.



Add fragments in range
It is a miscellaneous function to specify the fragmentation number at All
and Chain. Click the fragment in 3D view, that fragment No. is displayed
at No. field. Two or more fragments can be specified. Specify the distancefrom fragment at front of Å then by clicking the “Add” button, the86fragment No.s that in range are added at parameter fields.
There are two methods in calculation of distance. “Center of mass” iscenter of mass of fragments, ”The shortest interatomic” is The shortest
interatomic distance.


Sort by base/backbone(DNA)The displayed order sort by base/backbone.



Sort by Main/Side Chain
In case of multi layer calculation, it will be displayed in the oerder ofmain/side chains.

Fig2.113IFIE MAP Fragment Order panel

Graph
Display the graph that have a horizontal axis as fragment No. and a vertical axis
as IFIE value. The fragments No. is specified for the field. If two or more
fragments are specified display sum of these values. Label display at upper ofgraph. The range of value is specified as a vertical axis. By Clicking the ”Draw
Graph” button, display the graph. The example is shown in Fig2.115.

87

Fig2.114

Fig2.115

IFIE MAP Graph panel

Example of graph

When you take the mouse cursor on the graph, show the fragment No. and value.
Show the File menu in bellow.


Load CSV file
Load CSV file that saved by “Save CSV file”.

Save CSV file88

Save the file that format is CSV.


Save Image
Save the image file(png,jpg,tiff).

3) instructions


Apply
Display the MAP with parameters.



Reset
Reset the MAP.



Enlargement, Shrink and TranslateStructure Note
Display second structure or chain at upper/right of MAP.



Enlargement by mouse
The rubber band is appear by push the left button on mouse. When release thebutton, enlarge display area.



Display value
When you take the mouse cursor on the graph, show the fragment No. and value.

Highright fragment in 3D view
By clicking the right button of mouse on item, display highlighted thatfragments on 3D View.

89

2.8.

FILM Isosurface

Load FILM result file, specify the orbital and display isosurface. At first load thecheck point file then select Monitor→Film isosurface. Popup FILM window.

Fig2.116

FILM Window

901) Menu

File menu CloseClose the window.

2) Parameters

Data DirectorySpecify the folder that is stored result files. The convention of result filename isxxx_n_m.lmp2.（xxx:any、n.m fragment No.）。After specify the folder, load result
files and display Fragment Pair.



Fragment Pair
Display fragment pair. Select a fragment pair, display that orbital at Orbital. By
clicking ”Highlight fragments in 3D graphics” button then display thehighlighted fragment in 3D View.



Orbital
Select item(Inter Fragment/Inner Fragment/All/None) of Sort by energy.
Inter Fragment : list item are sorted by the energy between inter fragment.
Inner Fragment : list item are sorted by the energy between inner fragment.
All : list item are sorted by the energy of all pair.
None : Select the each orbital.
Display orbital number at Selected pairs and sum of energy between selected
orbitals at Calculate Energy. Two or more orbitals can be specified. Selected
orbitals is possible to edit. After edit this field, enter the return key then displaythat energy.
Maximum number of pairs list : Specify maximum number of orbital pairs inlist. It is available by pressing enter key.
If from 3D marked, when click the atom in 3D view, display related orbitals at
Selected pairs.
Selected orbitals : The starting track number of the selected orbital is set. It’s
editable, if you press the Return key, Sum of Energies will be calculated.
Sum of Energies : Display value which the total sum of the combination of theselected orbitals. Integrated target is Inter,Inner or All which is selected optionof Sort by energy.

91

Fig2.117

Example of Inter Fragment list

Fig2.118



Example of None

Display Matrix
Display energy matrix between orbitals on the other window. Display energythat included fragment by fragment order. The displayed color is changed from
red to white. Change min/max value and by Clicking “Apply” button, redisplay
matrix. When you take the mouse cursor on the matrix, show the orbital index
and energy. By Clicking item on matrix, set orbital index at “Selected orbitals”.
Click item with push control key, add orbital index. Ezample is showed in エラー! 参照元が見つかりません。.
There are three display types, ”Inner Frament”,”Inter Fragment” and ”All”.
Save image file(PNG,Tiff,JPG) by selecting File→Save Image menu.

Isosurface Parameter
The color of each fragment can be specified. phase
If draw two or more orbitals that have different phase so upset isosurface color,the color in each orbital can be specified according to the following instructions.
By clicking “Set” button, set parameters on selected orbital. Draw a isosurface, if

92upset isosurface color, select Color(+,-)

button and click Set button. Thissetting of each orbital is done, all orbital draw at the same time.


Draw
Draw isosurfaces that are selected.

DeleteDelete isosurface.

a) click at (25,48)b)

selected orbital pair on the list

Fig2.119

Example of Matrix

93

Fig2.120

Example of FILM isosurface

94

2.9.

Basic Action

2.9.1. Enlargement, Shrink, Rotation and Translate
A displayed figure can be enlarged, reduced, rotated and moved. Operations of eachaction are shown in Table 2.1.
Table 2.1 Operations of Enlargement, Shrink, Rotation and Translate(two buttons with windows)
ActionEnlargement
ShrinkRotationTranslate

Operation
Hold down the Alt key while clicking the left mouse button ,move the mouse pointer down.
Hold down the Alt key while clicking the left mouse button,
move the mouse pointer up.
Hold down the left mouse button, and move the mouse pointerin the direction you want to rotate.
Hold down the right mouse button, and move the mousepointer in the direction you want to move.

2.9.2. Coordinate Rotation and Translation of Molecule Structure
The coordinate rotation and translation of molecule structures each file can be input by
typing. This operation modifies the coordinates of molecule structures in the files asv
subjects, and is available for the editing of molecule structures.

n

The mark which shows the translation direction are displayed at the midpointof rotation like an example on the right. Key binds arezTranslation x direction (－:z＋:x), y direction( －:c＋:v), z direction(－:b＋:n)Rotation x axis (－:a＋:s), y axis (－:d＋:f), z axis(－:g＋:h).

The coordinate of the atom is modified when it is rotated and translated.

xbc

As for the translation, you can move the coordinate of the atom by 0.1Å each time
you press the key. To translate it by 0.5Å, hold down the Shift key, and to translate itby 1.0Å, hold down the Ctrl key. As for the rotation, you can rotate it through 1°each
time you press the key. To rotate it through 5, hold down the Shift key, and to move it
through45, hold down the Ctrl key.
When you input files, the center of the rotation is that of the gravity of the wholeatoms. The coordinate of the particular atom can be the center of rotation. To makethe position of an atom the center of rotation, click on the atom and select [Set File
Rotation Center] under [Tool] menu.
Without selecting, the center of rotation is set to that of the gravity of each atom byselecting [Set File Rotation Center] under [Tool] menu.

952.9.3. Control of visualization area
You can control visualization area by mouse wheel operation. Example is shown
Fig2.121. The operation controls the clip distance before and after the display according
to the amount of movement of the mouse wheel. In this way it will not be displayed
except the designated range. Just turn the wheel, then clip the front area, turn thewheel with Shift-key pressed, then clip the back area. Clip volume is 0.1 times bypressing with Control-key. With pressed Alt-key, then reset clip area.

upper: standard, lower : clip front and backFig2.121 Example of control clip area.

96

2.10. How to Select Structures as Subjects
When you click on molecular structures on viewing-window, the atom’s information isshown in a message area. And the structures as subjects are added colors in yellow
and highlighted in hierarchical window. Click on an atom or a residue and click onanother one while holding down the Shift key to select the intervening ones. Click on
an atom or a residue while holding down the Ctrl key to add it. This example of adisplay is shown in Fig2.122.
By clicking on names of a residue and an atom in hierarchical window, they can beselected. They are displayed in yellow on 3D view-window.

Click on an atom or aresidue and click on another one while holding down the Shift key to select theintervening ones.

Click on an atom or a residue while holding down the Ctrl key to

add it.

Fig2.122 Example of Selected Atoms

97

2.11. Setting Preference Categories
In the case that you click on atoms or residues with the right button on the mouse, thepop-up dialog box appears to specify each category: Display, Model, Color and Label.
Atoms dialog box is shown in Fig2.123 and Residues dialog box in Fig2.124.

Byclicking on the atom or residue in hierarchical window with the left button on the mouseand clicking on it with the right button on the mouse, the dialog box is displayed as well.
This assignment apply to the Atom and Structure.
Display : Specify the display, on or off
Model : In the case of residues, select the display model from None, Wire Frame, Eire
Frame with Fragment Bond, Ball & Stick, Stick, Ball & Wire and CPK. Whenyou select None, the residue is displayed in the model specified in the menu bar.
Label: Specify a label. In the case of atoms, the names and numbers can be selected. In
the case of residues, the names and the names with numbers can be selected
Color: Select the display color from None, Atom, Residue, Charged Residue, Atom
Charge, Fragment, Interaction Energy, Interaction Energy[lock], Chain, File andOther. When you select None, the residue is displayed in the color selected in themenu bar. In the case of Other, setting colors are displayed beside the button.
By clicking on it, a color preference dialog box is displayed.

Fig2.123 Display Atom Dialog Box

Fig2.124 Display Residues Dialog Box

982.12. Setting the Bounding box
The bounding box can be displayed using MOL2 file. Type “grid. file” above@<TRIPOS>ATOM and type the top of the coordinate with the proper atom. Specify
the line which you want to display with @<TRIPOS>BOND, in the index, then.
example of the display is shown as follows.

Fig2.125 Domain of Analysis Display

99

An@<TRIPOS>MOLECULE
test data
8 12
0
0
0
0
0
grid file@<TRIPOS>ATOM
1 N-8.0000 -4.0000
2 N
8.0000 -4.0000
3 N-8.0000 -4.0000
4 N
8.0000 -4.0000
5 N-8.0000 18.0000
6 N
8.0000 18.0000
7 N-8.0000 18.0000
8 N
8.0000 18.0000@<TRIPOS>BOND
1
1
2 1
2
2
4 1
3
3
4 1
4
3
1 1
5
5
6 1
6
6
8 1
7
7
8 1
8
7
5 1
9
1
5 1
10
2
6 1
11
3
7 1
12
4
8 1

-9.0000 N.4-9.0000 N.4
4.0000 N.4
4.0000 N.4-9.0000 N.4-9.0000 N.4
4.0000 N.4
4.0000 N.4

1
1
1
1
1
1
1
1

GLY
GLY
GLY
GLY
GLY
GLY
GLY
GLY

Fig2.126 Example of files for the Bounding box(g10a_grid.mol2)100

0.00000.00000.00000.00000.00000.00000.00000.00002.13. Molda
This section describes Creation DNA/RNA, Mutation DNA/RNA, and Adding Nucleotide
DNA/RNA. Refer to Molda Users Guide about other Molda.
2.13.1. Creation DNA(1) Molda Menu
Input DNA/RNA, Mutation DNA/RNA and Add Nucleotide DNA/RNA are added toModel menu.

Fig2.127 Molda Menu
(2) Input DNA sequence
Select [Molda]-[Input]-[DNA] menu. The menu is shown in Fig2.128. Create DNA dialog
box is displayed and shown in Fig2.129. For instance, input AAGGCCTT to the text
area of the dialog box as Input sequence and click OK. The text area has to input
DNA-bases: A, G, C and T. The result is displayed on Molda viewer and shown in
Fig2.130. The other chain will be created automatically.

Fig2.128 Input DNA menu

101

Fig2.129 Create DNA dialog box

Fig2.130 Result of create DNA

102

(3) To Viewer
If you want to display the DNA on BioStation main window then select [Display]-[To
Viewer] menu. The DNA is displayed on BioStation main window. Result of display isshown in Fig2.131.

Fig2.131 Result of display DNA on BioStation viewer

1032.13.2. Creation RNA(1) Input RNA sequence
Select [Molda]-[Input]-[RNA] menu. The menu is shown in Fig2.132. Create DNA dialog
box is displayed and shown in Fig2.133. For instance, input AAGGCCUU to the text
area of the dialog box as Input sequence and click OK. The text area has to input
RNA-bases: A, G, C and U. The result is displayed on Molda viewer and shown in
Fig2.134.

Fig2.132 Input RNA menu

Fig2.133 Create RNA dialog box

104

Fig2.134 Result of create RNA(2) To Viewer
If you want to display the RNA on BioStation main window then select [Display]-[To
Viewer] menu. The RNA is displayed on BioStation main window. Result of display isshown in Fig2.135.

Fig2.135 Result of display RNA on BioStation viewer

105

2.13.3. Mutation DNA(1) Display DNA on BioStation
Open pdb file of DNA on BioStation Viewer.

Fig2.136 Result of display pdb file of DNA on BioStation viewer(2) Display on Molda
Display the DNA on Molda. Select [File]-[Molda [with file]] menu of BioStation Viewer.
The DNA is displayed on Molda. It is shown in Fig2.137.

Fig2.137 Result of display DNA on Molda

106

(3) Select nucleotide
Select [View]-[Sequence Viewer] menu and Sequence Viewer is displayed. Select amutated nucleotide and click OK on Sequence Viewer. The selected nucleotide changes
the color to cyan on Molda. For instance, select DC3 and click OK on Sequence Viewer.
It is shown in Fig2.138 and Molda is shown in Fig2.139.

Fig2.138 Selected DC3 on Sequence Viewer

Fig2.139 Selected DC3 on Molda

107

(4) Mutate DNA
Select [Molda]-[Point Mutation]-[DNA] menu. The menu is shown in Fig2.140.
Mutation DNA dialog box is displayed and shown in Fig2.141. If selected DC3 in (3)mutate into DT then select DT from the combo box of the dialog box and click OK. The
combo box has DNA-bases: DA, DG, DC and DT. The result is displayed on Molda
viewer and shown in Fig2.142.

Fig2.140 Point Mutation DNA menu

Fig2.141 Point Mutation DNA dialog box

Fig2.142 Result of Mutation DNA

108

(5) To Viewer
If you want to display the DNA on BioStation main window then select [Display]-[To
Viewer] menu. The DNA is displayed on BioStation main window. Result of display isshown in Fig2.143.

Fig2.143 Result of display DNA on BioStation viewer

109

2.13.4. Mutation RNA(1) Display RNA on BioStation
Open pdb file of RNA on BioStation Viewer.

Fig2.144 Result of display pdb file of RNA on BioStation viewer(2) Display Molda
Display the RNA on Molda. Select [File]-[Molda [with file]] menu of BioStation Viewer.
The RNA is displayed on Molda. It is shown in Fig2.145.

Fig2.145 Result of display RNA on Molda

110

(3) Select nucleotide
Select [View]-[Sequence Viewer] menu and Sequence Viewer is displayed. Select amutated nucleotide and click OK on Sequence Viewer. The selected nucleotide changes
the color to cyan on Molda. For instance, select U2 and click OK on Sequence Viewer. It
is shown in Fig2.146 and Molda is shown in Fig2.147.

Fig2.146 Selected U2 on Sequence Viewer

Fig2.147 Selected U2 on Molda

111

(4) Mutate RNA
Select [Molda]-[Point Mutation]-[RNA] menu. The menu is shown in Fig2.148. Mutation
RNA dialog box is displayed and shown in Fig2.149. If selected U2 at (3) mutate into A
then select A from the combo box of the dialog box and click OK. The combo box has
RNA-bases: A, G, C and U. The result is displayed on Molda viewer and shown in
Fig2.150.

Fig2.148 Point Mutation RNA menu

Fig2.149 Point Mutation RNA dialog box

Fig2.150 Result of Mutation RNA

112

(5) To Viewer
If you want to display the DNA on BioStation main window then select [Display]-[To
Viewer] menu. The RNA is displayed on BioStation main window. Result of display isshown in Fig2.151.

Fig2.151 Result of display RNA on BioStation viewer

113

2.13.5. Adding Nucleotides of DNA
In the Adding Nucleotides of DNA you can choose position from 5’Terminal, 3’Terminal
and Middle. This section describes each positions.
2.13.5.1 Position：5’Terminal
If you want to Adding Nucleotides in 5'-end direction then select 5’Terminal.
(1) Display DNA on BioStation
Open pdb file of DNA on BioStation Viewer. The following display properties are setting
for describing: [Model]-[Atom (A)] sets Off, [Model]-[Structure(S)] sets Cα[line], and[Tool]-[Label]’s Residue Label sets on.
For instance, if a base pair of B chain’s DC9 is missing then add DG in 5'-end direction
as next to DA1 on A chain.

Fig2.152 Result of display pdb file of DNA on BioStation viewer

114

(2) Display Molda
Display the DNA on Molda. Select [File]-[Molda [with file]] menu of BioStation Viewer.
The DNA is displayed on Molda. It is shown in Fig2.153.

Fig2.153 Result of display DNA on Molda(3) Select starting DNA-base for Add
Select [View]-[Sequence Viewer] menu and Sequence Viewer is displayed. Select astating nucleotide and click OK on Sequence Viewer. The selected nucleotide changes
the color to cyan on Molda. For instance, select DA1 and click OK on Sequence Viewer.
It is shown in Fig2.154 and Molda is shown in Fig2.155.

Fig2.154 Selected DA1 on Sequence Viewer

115

Fig2.155 Selected DA1 on Molda

116

(4) Adding Nucleotide
Select [Molda]-[Add Nucleotide]-[DNA] menu. The menu is shown in Fig2.156. DNA
Adding Nucleotide dialog box is displayed and shown in Fig2.157. If DG adds next to
DA1 in 5’-end direction then choose 5’Terminal from Position, input G to the text area
as Sequence and click OK. Sequence has to input DNA-bases: A, G, C and T. The result
is displayed on Molda viewer and shown in Fig2.158.

Fig2.156 DNA Add Nucleotide menu

Fig2.157 DNA Add Nucleotide dialog box

117

Fig2.158 Result of DNA Adding Nucleotide
Remark・ If selected chain in (3) has only one DNA-base then it doesn’t allow you to add
any nucleotides to the chain.
・ If the Position selects 5’Terminal then selected DNA-base in (3) has to be on
5’-end.

118

(5) To Viewer
If you want to display the DNA on Molda to BioStation main window then select[Display]-[To Viewer] menu. The DNA is displayed on BioStation main window. Resultof display is shown in Fig2.159.

Fig2.159 Result of display DNA on BioStation viewer

1192.13.5.2 Position：Middle
If you want to add nucleotides in 3'-end direction and selected DNA-base isn’t on 3’-end
then select Middle.
(1) Display DNA on BioStation
Open pdb file of DNA on BioStation Viewer. The following display properties are setting
for describing: [Model]-[Atom (A)] sets Off, [Model]-[Structure(S)] sets Cα[line], and[Tool]-[Label]’s Residue Label sets on.
For instance, if two base pair of A chain’s DG2 and DC3 are missing then add DG and
DC in 3'-end direction as next to DA5 on B chain.

Fig2.160 Result of display pdb file of DNA on BioStation viewer

120

(2) Display Molda
Display the DNA on Molda. Select [File]-[Molda [with file]] menu of BioStation Viewer.
The DNA is displayed on Molda. It is shown in Fig2.161.

Fig2.161 Result of display DNA on Molda

121

(3) Select starting DNA-base for Adding
Select [View]-[Sequence Viewer] menu and Sequence Viewer is displayed. Select astating nucleotide and click OK on Sequence Viewer. The selected nucleotide changes
the color to cyan on Molda. For instance, select DA5 and click OK on Sequence Viewer.
It is shown in Fig2.162 and Molda is shown in Fig2.163.

Fig2.162 Selected DA5 on Sequence Viewer

Fig2.163 Selected DA5 on Molda

122

(4) Add Nucleotide
Select [Molda]-[Add Nucleotide]-[DNA] menu. DNA Add Nucleotide dialog box isdisplayed and shown in Fig2.164. For instance, if DG and DC adds next to DA5 in 3’-end
direction then choose Middle from Position, input GC to the text area as Sequence andclick OK. Sequence has to input DNA-bases: A, G, C and T. The result is displayed on
Molda viewer and shown in Fig2.165.

Fig2.164 DNA Add Nucleotide dialog box

Fig2.165 Result of DNA Adding Nucleotide123Remark・ If selected chain in (3) has only one DNA-base then it doesn’t allow you to add
any nucleotides to the chain.
・ If the Position selects Middle then selected DNA-base in (3) has to be on 5’-endor middle, not on 3’-end.
・ If the Position selects Middle then add nucleotides equal or less than number ofmissing nucleotides.
(5) To Viewer
If you want to display the DNA on BioStation main window then select [Display]-[To
Viewer] menu. The DNA is displayed on BioStation main window. Result of display isshown in Fig2.166.

Fig2.166 Result of display DNA on BioStation viewer

1242.13.5.3 Position：3”Terminal
If you want to add nucleotides in 3'-end direction and selected DNA-base is on the 3’-end
then select Middle.
(1) Display DNA on BioStation
Open pdb file of DNA on BioStation Viewer. The following display properties are setting
for describing: [Model]-[Atom (A)] sets Off, [Model]-[Structure(S)] sets Cα[line], and[Tool]-[Label]’s Residue Label sets on.
For instance, if a base pair of B chain’s DA4 is missing then add DT in 3'-end direction
as next to DG3 on A chain.

Fig2.167 Result of display pdb file of DNA on BioStation viewer

125

(2) Display Molda
Display the DNA on Molda. Select [File]-[Molda [with file]] menu of BioStation Viewer.
The DNA is displayed on Molda. It is shown in Fig2.168.

Fig2.168 Result of display DNA on Molda

126

(3) Select starting DNA-base for Adding
Select [View]-[Sequence Viewer] menu and Sequence Viewer is displayed. Select astating nucleotide and click OK on Sequence Viewer. The selected nucleotide changes
the color to cyan on Molda. For instance, select DG3 and click OK on Sequence Viewer.
It is shown in Fig2.169 and Molda is shown in Fig2.163.

Fig2.169 Selected DG3 on Sequence Viewer

Fig2.170 Selected DG3 on Molda

127

(4) Add Nucleotide
Select [Molda]-[Add Nucleotide]-[DNA] menu. DNA Add Nucleotide dialog box isdisplayed and shown in Fig2.171. For instance, if DG and DC adds next to DG3 in 3’-end
direction then choose 3’Terminal from Position, input T to the text area as Sequenceand click OK. Sequence has to input DNA-bases: A, G, C and T. The result is displayedon Molda viewer and shown in Fig2.172.

Fig2.171 DNA Add Nucleotide dialog box

Fig2.172 Result of DNA Adding Nucleotide

128

Remark・ If selected chain in (3) has only one DNA-base then it does not allow you to add
any nucleotides to the chain.
・ If the Position selects 3’Terminal then selected DNA-base in (3) has to be on the
3’ -end.
・ If the Position selects 3’Terminal and the selected nucleotide dose not haveprevious nucleotide, first add missing nucleotides by Middle and then add
nucleotides in 3’-end direction on the 3’-end.
(5) To Viewer
If you want to display the DNA on BioStation main window then select [Display]-[To
Viewer] menu. The DNA is displayed on BioStation main window. Result of display isshown in Fig2.173.

Fig2.173 Result of display DNA on BioStation viewer

1292.13.6. Adding Nucleotides of RNA
Adding Nucleotide of RNA’s operations are same as DNA’s.
This section describes Adding Nucleotide of RNA when the Position is chosen Middle.
(1) Display RNA on BioStation
Open pdb file of DNA on BioStation Viewer. The following display properties are setting
for describing: [Model]-[Atom (A)] sets Off, [Model]-[Structure(S)] sets Cα[line], and[Tool]-[Label]’s Residue Label sets on.
For instance, if between G3 and C8 nucleotides are missing then add three nucleotides
in 3'-end direction as next to G3.

Fig2.174 Result of display pdb file of RNA on BioStation viewer

130

(2) Display Molda
Display the DNA on Molda. Select [File]-[Molda [with file]] menu of BioStation Viewer.
The DNA is displayed on Molda. It is shown in Fig2.175.

Fig2.175 Result of display RNA on Molda

131

(3) Select starting RNA-base for Adding
Select [View]-[Sequence Viewer] menu and Sequence Viewer is displayed. Select astating nucleotide and click OK on Sequence Viewer. The selected nucleotide changes
the color to cyan on Molda. For instance, select G3 and click OK on Sequence Viewer. It
is shown in Fig2.176 and Molda is shown in Fig2.177.

Fig2.176 Selected G3 on Sequence Viewer

Fig2.177 Selected G3 on Molda

132

(4) Add Nucleotide
Select [Molda]-[Add Nucleotide]-[DNA] menu. The menu is shown in Fig2.178. DNA
Add Nucleotide dialog box is displayed and shown in Fig2.179. For instance, if A, G and
U add next to G3 in 3’-end direction then choose Middle from Position, input AGU to thetext area as Sequence and click OK. Sequence has to input RNA-bases: A, G, C and U.
The result is displayed on Molda viewer and shown in Fig2.180.

Fig2.178 RNA Add Nucleotide menu

Fig2.179 RNA Add Nucleotide dialog box

133

Fig2.180 Result of RNA Adding Nucleotide
Remark・ If selected chain in (3) has only one RNA-base then it dose not allow to add any
nucleotides to the chain.
・ If the Position selects 5’Terminal then selected RNA-base in (3) has to be on the
5’-end.
・ If the Position selects Middle then selected RNA-base in (3) has to be on the
5’-end or middle, not on the 3’-end.
・ If the Position selects Middle then add nucleotides equal or less than number ofmissing nucleotides.
・ If the Position selects 3’Terminal then selected RNA-base in (3) has to be on the
3’-end.
・ If the Position selects 3’Terminal and the selected nucleotide dose not haveprevious nucleotide, first add missing nucleotides and then add nucleotides in
3’-end direction on the 3’-end.

134

(5) To Viewer
If you want to display the RNA on BioStation main window then select [Display]-[To
Viewer] menu. The RNA is displayed on BioStation main window. Result of display isshown in Fig2.181.

Fig2.181 Result of display RNA on BioStation viewer

1353. Examples of How to use
3.1.

Displaying the Results of ABINIT-MP Calculations.

Use the sample data which is operating at the Web site of ABINIT-MP(http://www.fsis.iis.u-tokyo.ac.jp/en).
oThe sample data are

the sample data of ( Gly) 10 g10a.zip 803 KB,
 g10a.cpf, Check point file of the FMO-HF/STO-3G calculation
 den.inp, input data for the calculation of the electron density
 g10a_fmo_sto-3g_3.den , grid data of the electron density
 g10a_fmo_sto-3g_3.map ,electrostatic potential map data on theelectron density
 g10a_fmo_sto-3g_4.esp , grid data of electron potential
 g10a_fmo_sto-3g_3.mo , grid data of molecular orbitals
 g10a_grid.mol2, data file of a display example for the domain
 g10a_fmo_sto-3g_3.efv, grid data of electron field vector

3.1.1. Displaying Molecular Structures
Start the Viewer and load g10a.cpf . An example of this display is shown in Fig3.1.
When the Viewer is started, molecular structures are displayed in the wire frame
model.

Fig3.1 Example of Display: g10a.cpf
From the Model menu, select Wire frame, Wire frame(with fragment bond)(specifying
frame for colors),Ball & Stick, Ball & Wire, CPK, Backbone, C, Ca (line) and C(tube)
to modify the model. Here are the resulting displays in Fig3.2- Fig3.8
136

Fig3.2 Wire Frame

Fig3.3 Wire frame model(with fragment bond)Fig3.4 ball and stickFig3.5 Ball & Wire model137

Fig3.6 CPK

Fig3.8 CLine model

Fig3.7 Backbone model

Fig3.9138

Stick(with boundary)3.1.2.

Changing Colors

From the Color menu, select Atom, Residue, Charged Residue, Atom Charge,
Fragment, and Chain to change the display color. Here are the resulting displays in
Fig3.10-Fig3.14.

Fig3.10 Adding Colors by Atom Type Fig3.11 Adding Colors by Residues

Fig3.12 Adding Colors by residue Charge

Fig3.13 Adding Colors by Chrges Atoms

139

Fig3.14 Adding Colors by fragment Fig3.15 Adding Colors by Chains ( one color
with one chain)

Fig3.16 Adding Colors by the Interaction Energy between Fragments. The Second
Fragment in Yellow is Displayed as a Reference.

1403.1.3. Adding Labels
When you select [Tool]-[Label], a dialog box to add labels is displayed.

Fig3.17 shows

an example with labels of residues in, and Fig. 3.19 shows it with those of atoms.

Fig3.17 Residue Lables Fig3.18 Molecules with Labels of Atoms ( names ofatoms)

1413.1.4. Displaying the Isosurface of the Electron Density
Load g10a_fmo_sto-3g_3.den with [File]- [Open]. A dialog box for the isosurface
is displayed, which value is generated in the file. Clicking on the Ok button lets
the isosurface of the electron density display. The example is shown in Fig3.19.
Select [File]–[File List], and the list of input files is displayed. Here, click on the Valuebutton beside g10a_fmo_sto-3g_3.den.

Since a dialog box for the isosurface value isdisplayed, change colors. When you click on the button beside Color, a color preference
dialog box is displayed. Here, select the appropriate color. The example is shown in
Fig3.20.

Fig3.19 Isosurface

Fig3.20 Isofurface with the Color
ChangedWhen you select [File]–[Delete File List], the list of input files is displayed. Here,select g10a_fmo_sto-3g_3.den and click on the Ok button. The isofurface is deleted.

1423.1.5. Adding Colors to the Isosurface of the Electron Density by the Value ofElectrostatic Potentia.
Load g10a_fmo_sto-3g_3.map with [File]- [Open]. An electrostatic potential dialog
box appears on the screen. Set Min Max to -0.05 0.05. Clicking on Ok lets theisofurface of the electron density display. This example is shown in Fig3.21.
You can change the transparency of the isosurface. Selecting [File]–[File List] lets
the list of the input file displayed. Here, click on the Value button beside
g10a_fmo_sto-3g_3.map.

Since electrostatic potential dialog box is displayed, set

Transparency to 50. Select [Color]–[Atom]–[Charge]–[Atom] as well. This example isshown in Figure 3.23.

Fig3.21 Adding Colors to the Isosurface of

Fig3.22 Changed the Transparency of

the Electron Density by the Value ofIsosurface

Electrostatic Potential1433.1.6. Isosurface of Electrostatic Potential
Load g10a_fmo_sto-3g_4.esp with [File]-[Open]. An electrostatic potential dialog
box is displayed. When you set Transparency to 50 and click on the Ok button, theisofurface value of electrostatic potential is displayed.

The example of molecule

structures with Stick is shown in Fig3.23.

Fig3.23 Isosurface of Electrostatic Potential144

3.1.7.

Isosurface of Molecular Orbitals

Load g10a_fmo_sto-3g_3.mo with [File]- [Open]. A molecular orbital dialog box isdisplayed. Here, when you select an orbital that you want to display from the graphic
and click on draw, the isosurface of the molecular orbital is displayed.

This example

shows the isosurface of the first fragment, LUMO, which is shown in the Fig3.24.

Fig3.24 Isosurface of Molecular Orbitals

145

3.1.8. Electron field vector
Load g10a_fmo_sto-3g_4.efv with [File]-[Open]. Display the electron field vector by
default options. （Fig3.25）
Next is a example which changes options. Min,Max の値を-0.1,0.1 にします。Set section
options to, B set –27 and select Density for value.By clicking Draw button, the section isdisplayed(Fig3.27). An option dialog is shown in Fig3.26.
Set the next Model of molecular structure to Ball&Stick, transparency to 50, modelof vector to Stick and Number of step to 150. by Clicking Draw button, an example ofstick vector is displayed(Fig3.29). Since the number of steps was increased, an electricfield vector is displayed from lower Glycine(+) to upper Glycine(-).

Fig3.25 Example of electron field vector

146

Fig3.26 Section dialog box

Fig3.27 Example of vector with section

147

Fig3.28 Electron field vector dialog box

Fig3.29 Example of stick vector

148

3.2.

Example of Structures of Estrogen Receptors – Ligand Complexes

Visualizing structures with using sample data. Use estrogen receptors- ligand
complexes as the sample data, located in the folder, sample. Use the pdb file,
ERE_EST.pdb and ERR_RAL.pdb, of the bond between an agonist as a ligand, 17β-estradiaol and a selective agonist, raloxifene.
3.2.1. Peptide Chains in the the C Line Model
Start the Viewer and load ERE_EST.pdb. Default model is [Model(Atom)]-[Off],[Model(Structure)]- [Cα Line]. This example is shown in Fig3.30.
The another model examples are shown in Fig2.31-Fig2.37.

Fig3.30 Molecular Structures149

3.2.2.

Modifying the model of C Line of Peptide and the model of Ligands

Select [Selection]-[Residue] and click on the ligand with the left mouse button. Fig3.31
shows an example of the highlighted a ligand which you click.

Fig3.31 Highlighted a Ligand150

Next, click on the ligand by the right mouse button. Since a dialog box for specifying
residues is displayed, select Atom in the Color and Ball & Stick in the Model option andclick on the Ok button. (Fig3.32) This allows you to display a ligand in the Ball & Stickmodel. This example is shown in Fig3.33.

Fig3.32 Displaying Residue Dialog Box

Fig3.33 Ligand in the Ball & Stick Model151

Next, click on the ligand with the right mouse button and select CPK in the Model
option of the residue dialog box.

Set other in the Color option and select theappropriate color by clicking on the side button. The ligand is displayed with colors
selected in the space-filling model. This example is shown in Fig3.34.

Fig3.34 Ligand in the Space Filling Model152

3.2.3. Display Peptide Chains in the CLine Model+ Ligands+ Selected Residues
You can display residues around ligands in the Wire Frame model. Click on the four
residues around ligands ( ASN519～GLU523 in this example ) with the left button on
the mouse while holding down the Shift. Click on the one of them with the right mousebutton while holding down the Shift. Since the Residue dialog box is displayed, selectWire Frame in the Model and click on the Ok button.

This displays the selected

residues in the Wire Frame model. This example is shown in Fig3.35.

Fig3.35 Selected Residues in the Wire Frame

153

Next, you can change the display from hierarchical window.

Click on residues

around ligands. Since the selected residues in hierarchical window are highlighted,
click onbeside the names of residues and close the current display of the residues.

And then, click on this residue again and the residue below five ones (GLY420～
PHE425 in this example ) while holding down the Shift. Here, some residues are
selected. Next, click on the selected residues with the right button on the mouse.
Since the Residue dialog box is displayed, select Wire Frame in the Model and click on
the Ok button.

This displays the selected residues in the Wire Frame model. This

example is shown in Fig3.36.

Fig3.36 Residues Selected in Tree figure in the Wire Frame Model154

3.2.4.

Display Ligands and Charged Residues

You can display the whole residues in the Wire Frame model by selecting[Model(Atom)]-[Wire Frame] and [Model(Structure)]-[Off].

Select [Tool]-[Display

Selected Residue]. Since the residue dialog box appears, click on Unselect All and selectcharged residues (ASP,GLU,LYS,ARG). This allows you to display the only charged
residues which you select.

This example is shown in Fig3.37.

which is selected optionally can be displayed as well.

Fig3.37 Charged Amino Acid155

The only residue

When you select [Color(Atom)]-[Charged Residue], the displayed residues are added
colors by the charged values. This example is shown in Fig3.38.

Fig3.38 Residues Added Colors by Charged Amino Acid
Select [Tool]-[Display Selected Residue].

Since the residue dialog box appears, click on

Select All. The setting of residues is unspecified, which displays the whole residues.
This example is shown in Fig3.39.

Fig3.39 All the Residues Added Colors by Charged Amino Acid156

3.2.5.

Display Atoms around Ligand in specified Distance

Click on the ligand and select [Tool]-[Display Atom in Distance].

Since the dialog box

for the assignment of a distance appears, select Residue from From selected and input 4
in the Distance. And then, atoms within 4Å from the ligand are displayed. This
example is shown in Fig3.41. Here, click on the atom around the center of the ligand
and select [Tool]-[Set Rotation Center]. This makes you move the display easier, since
the center of the rotation can be the selected atom.

Fig3.40 Atoms in the Distance Dialog Box

Fig3.41 Atoms within the Distance157

Next, you can display the distance between atoms. Select [Color]-[Atom] to set colors
to the whole atoms. Click on the ligand with the right button on the mouse and set itin the Ball & Stick model. Here, select [Monitor]-[Distance]. Click on the hydrogenof a side of the ligand. Next, click on the nearby oxygen. This displays the distance
between the atoms in the message area. This example is displayed in Fig3.42.

Fig3.42 Distance between the Atoms

158

3.3.

Example of the Display of Interaction Energy between Fragments

Use the result of computations of the estrogen receptor – the ligand complex. With
the calculation as 1fragment = 1 residue, the interactions between residues andbetween residues and ligands can be displayed.
3.3.1. Load File
Start the Viewer and load ERD_EST.cpf. This display is shown in Fig3.43.

Fig3.43 Molecular Structure from the Input File159

3.3.2. Assignment of Interaction Energy between Fragments
Click on a ligand, EST600, in hierarchical window with the left mouse button. Select[Monitor]-[Interfragmnet Interaction]-[1:1] and popup the dialog box for the values ofinteraction energy (Fig3.44.).

Here, type min:-10, max:10 and click on the Ok button.

This allows you to display molecular structures, which are added colors to theinteraction energy between each residue from ligands within the range, -10 ～10kcal/mol. An example of the display is shown in Fig3.45.

Fig3.44 Interaction Energy between Fragments Dialog Box

Fig3.45 Interaction Energy between Fragments Display

160

3.3.3. Assignment of ThresholdTo highlight ligands, a display attribute dialog box is displayed by clicking on ＥＳＴ
600 in hierarchical window with the right mouse button. Here, click on the button in
the Color to select the proper color and specify CPK in the Model (Fig3.46) Next, select[Monitor]-[Interfragment Interaction]-1:1[lock] and put 2 in the threshold at the dialog
box for values. This makes it impossible to display residues with absolute values of theinteraction energy under 2kcal/mol. An example of the display is shown in Fig3.47.

Fig3.46 Display Attribute for Ligands Dialog Box

Fig3.47 Interaction Energy between Fragments, Specifyed Threshold Display

161

3.3.4. Interaction Energy between Selected Fragments
Select [Model(Atom)]-[Stick].

Select [Monitor]-[Interaction Energy].

Menu isdisplayed in green until this menu is selected again. And by selecting the display, theinteraction energy between selected fragments (residues) is displayed. An example ofthe display by clicking on the ligands and fragments around them is shown in Fig3.48.
In addition, the interaction energy list between fragments (residues) can be displayed
as Fig2.66.

Fig3.48 Interaction Energy between Selected Fragments Display

162

3.4.

How to Overlay

Use data of ERE_EST.cpf and ERR_RAL.cpf to overlay.
3.4.1. Load File
Start the Viewer and select [Model(Structure)]-[C, [Color(Structure)]-[File] andload ERE_EST.cpf , ERR_RAL.cpf. This allows you to set colors to the molecules eachfile. An example of the display is shown in Fig3.49.

Fig3.49 Two Molecules Load from the Files163

3.4.2. Overlay with All the CCoordinate
Select [Tool]-[Overlay Molecules]. Popup A dialog box for the overlay. As you use thedefault value, click on the Ok button. In the default, overlay the molecules each filewith the C  coordinate. An example of a display after the overlay is shown in Fig3.50.
Since all over the molecules are overlaid, they are not lined up on the whole.

Fig3.50 Molecules Overlaid Each File with the C Coordinate
3.4.3. Overlay by Atom(C within Selected Residues)
Next, you can overlay molecules by selecting 3 atoms(C . Select [Tool]-[Overlay
Molecules].

Set Residue in the Type, and C  in the Method. Click on 3 parts of eachresidue, which is similar to each other structurally by turns. The residue numbers,
which you click are displayed in the input field, where you can modify them by using the
key board.
keyboard.

In the case that you put the wrong number, it can be deleted by theThis dialog box is shown in Fig3.51.

Here, click on the Ok button.

Display both ligands (EST600 and RAL600) in the Stick model.

You can see thedifference of the position of Herix 12 in the end side, C, of both agonist (EST pink) andantagonist (RAL purple).(Fig3.52)

164

Next, select [Model]-[C{tube}]. An example of the display is shown in Fig3.53.

Fig3.51 Overlay Molecules Dialog Box

Fig3.52 The Result of Molecules Overlaid by Selected Residues

165

Fig3.53 The Result of Molecules Overlaid by Selected Residues (C{tube})

166

3.5.

Example of How to Add Hydrogen

Use a sample file (ERE_EST_noH.pdb) with hydrogen removed in advance. In orderto add hydrogen, Reduce needs to be preconditioned to be installed.

Refer to thesetting of Reduce in Section 4.5 so as to install.
Load ERE_EST_noH.pdb and select [Tool]-[Add Hydrogen]. Popup a dialog box toadd hydrogen. (Fig3.54). Input file name added _addH is displayed in the output file
field as a default. In the Options, ｓet options which can be used in Reduce. By click on
the Ok button, a display of a command prompt is displayed to appear a log for the
execution. Input exit to close the window.(Fig3.55)

Fig3.54 Add Hydrogen Dialog

Fig3.55 Command Prompt Window

167

When you close the command prompt, you could be asked if you want to display the
result or not. Here, clicking on the Ok button lets the display replace it with addedhydrogen.

Fig3.56 Confirmation of Displaying the Result

Fig3.57 Molecule Structure Added Hydrogen

168

3.6.

Example of Interfragment interaction energy N:1

Display an example of Interfragment interaction energy N:1
calculation

results

of

DNA

and

protein.

By

load

a

using of thesamplefile,trunc-DB7_Hopt_moe_DNA.cpf, display molecular structures with the Cα[tube] model.
By selecting [Monitor]- [Interfragment Interaction]-[N:1], pop up a dialog box. This dataconsist of protein(fragment number 23-222), lagend (223) and DNA(1-22). In order toshow Interaction energy between protein, ligand and DNA, input 23-223 for the Base
fragment, and set Min,Max to -100,100, By clicking on OK button, protein, ligand andDNA are colored by the value of interaction energy. Red parts are stable relations.

Fig3.58 Example of Interfragment interaction energy N:1

169

3.7.

Example of trajectory

3.7.1. Glyine
By loading a sample file, G05A.trj, molecular structure at first step(Fig3.59) isdisplayed. Clicking on the

button lets the trajectory of molecular structure

display. The Molecular structure at the last step is shown in Fig3.60.

Fig3.59 Molecular structure at the first step

Fig3.60 Molecular structure at the last step170

3.7.2. Si8
By loading a sample file, dyna_pot_test.tr2. Nano scale device simulation team of
Frontier Simulation Software for Industrial Science provided this result. This is Si8 MD
calculation result. It edits every ten steps for this display example. The vector expresses
the force in which it is influence on an atom. Please specify [Model(Atom)]-[Wire Frame],
Model(Atom)→Wire Frame 、Preference→Set Preferences→Arrow(Trajectory) arrow
scale property is 10 in preference dialog. The first step is shown in Fig3.61. Clicking on
thebutton lets the trajectory of the vector animation. The last step is shown in

Fig3.62.

Fig3.61 The first step of vector example.

171

Fig3.62 The last step of vector example.

3.7.3.

Create a movie file of trajectoryThis section explains ho to make a movie file by using FFmpeg that is free software.
１) Open file
Open a trajectory file by selecting File→Open. In this case, when Trajectory file isselected with Files of Type, it becomes easy to choose filing because only trajectory
file is displayed in the list. After load the file, popup the trajectory window.
２) Specify options
If you want to add color by fragment, select Color→fragment menu on main window.
Set resolution options of Ball, Stick, CPK and Tube to 64 by Preferencemenu(Preferences→Set Preference→Resolution), It becomes nice to visualize amolecular model. By selecting Disable at Preferences →Display Axis、then the xyz
axis at lower/left in window disappear.
３) Create image files
Specify the folder that is saved image files (File→Create image files menu) Format
of images is JPEG. Convention of file name is sequential number for six digits.
４) Prepare to create a movie file
The source code of FFmpeg can be downloaded from http://ffmpeg.org/. The
executable file for windows can be downloaded from http://blog.k-tai-douga.com/.

172

Copy ffmpeg.exe to C:¥Program Files¥ffmpeg, the copied folder is added to theend of PATH like bellow.
;C:¥Program Files¥ffmpeg
It is useful to execute the ffmpeg without specified install folder.
５) Create a movie file
Please type in bellow command at the folder that is stored image files by usingcommand prompt. It is easy to change folder to drag the folder from explorer.
ffmpeg -r 75 -i "image%06d.jpg" -vcodec wmv2 -sameq -s 640x480
out_r75_640x480.wmv-r 75 ：set frame rate（frame per 1 second） to 75（default value is 25）.
-i "image%06d.jpg"： Spceify image file name. %06d means sequential
number for six digits.
-vcodec wmv2 ： set Windows Media Video as codec. If you specify mjpeg or
mspeg4v2(MS-MPEG4), according to PC you can not play this file on PowerPoint. So
you may not specify this option.
-s 640x480: Specify size of screen 640x480. if not specify this option, output size
is same size of input. You had better specify this option if input size is bigger.
Because it puts a strain in CPU.
-sameq：Image quality of output is same quality as input.
out_r75_640x480.wmv： output file nameffmpeg -h > ffmpeg.txt : output help
ffmpeg -formats > formats.txt : output format
６) Attach a movie file on PowerPoint
Select menu Insert→Video→File.
It is only to link the file, so if you copy the PowerPoint file, you have to copy themovie file with it.
Reference1) http://opensourceaki.blogspot.com/2007/10/ffmpeg_19.html
2) 原一浩、寺田学、本間雅洋、足立健誌、堀内康弘、堀田直孝、月村潤、尾花衣美、FFmpeg
で作る動画共有サイト（毎日コミュニケーションズ、2008）

173

3.8.

Example of crystal

Load the Gaussian Cube file that includes the atomic structure of a Bi super-thin film
(four layers), and the electron density in order to visualize an isosurface and a periodic
display. Nano scale device simulation team of Frontier Simulation Software forIndustrial Science provided this result.
3.8.1. Load a file and visualize the isosurface
Load a sample file(4LBi.cube) and choose Density for the file type because this fileincludes electron density data. Next, set Ball&Stick to the mode, isosurface value to0.009, transparency to 50 and Bonding box to on. The dialogs and the result display are
shown in Fig3.63～Fig3.65.

Fig3.63 File type dialog

Fig3.64 Isosurface dialog

Fig3.65 Example of isosurface of electron density1743.8.2. Periodic display
By selecting [Viewpoint]-[Periodic], popup a dialog box to specify periodic options. Ｔｈe
example file is Gaussian Cub, so there are a three input fields for each X,Ｙ and Z
Interval. The value from the file is specified by the default. Ｘ and Ｙ Nums are to 2,
and clicking Draw button. Then each direction X and Y is displayed two times. The colorof bounding box is to cyan. A display result is shown in Fig3.66

Fig3.66 Example of periodic display
3.8.3. Display a section
By clicking Set button on the isosurface dialog box, pop up the section dialog and display
a half-transparent section on 3D window. Move a position of Z direction a little by slider
and set Color Range Min to 1.0E-3. By clicking Draw Button, a section displayed.

175

Fig3.67 Section dialog and example of section
Next, set Type to Line, Number of lines to 32. By clicking Draw button, isolines are
displayed.

Fig3.68 Example of isolines

176Set Type to Fringe, Color Min to 1e-3. Since the way to add colors to the section and theisosurface is same, color of them is the same.

Fig3.69 Example of isosurface colored by minimum and maximum value

177

3.8.4. Display bond
By selecting [Preference]-[Set Preference], pop up a dialog box to specify preference.
Set Scale of Connect Atom to 1.1, select Covalent , set resolution of balls to 16. Byclicking Apply button, atom bonds appear and the atom rendering is smooth.

Fig3.70 Change connect scale and ball resolution

178

3.9.

Example of CHPICHPI27)is developed by Dr. Umezawa(Microbial Chemistry Research Center)、Dr.

Nishio(CHPI Institute) and Microbial Chemistry Research Foundation. If you write
a paper by using this function, please describe to refer No.27. BioStationViewer
supports to edit parameters, execute program and display result. Please refer thebook “The CH/π Interaction” about detail of CH/π Intereaction.
At first load PDB file, and select Tool→CHPI then popup CHPI Dialog.
If you use default parameters, just clicking the “Execute CHPI Program” button,
to execute the program and display result. Explain parameters as below.
3.9.1.

Method for exploring XH/π contacts

(a)

(b)

I'


Datm

X

H

Dlin

Dpln
.

A1


O I

region 2

region 1

Dmax
J

A2

region 3

O
A1

Fig3.71 Method for exploring XH/π contacts

Method for exploring XH/π contacts (the six-membered aromatic ring is shown as anillustrative example). (a) O: centre of the π-plane. A1 and A2: nearest and second nearest
sp2-atoms, respectively, to the hydrogen H. : dihedral angle defined by A1OA2 and HA1A2
planes. : X-H-I’ angle. Dpln: perpendicular distance between H and the π-plane (H/I). Datm:
HA1 distance. Dlin: distance between H and the line A1-A2 (H/J). (b) Regions to be searched.
Region 1: zone where H is above the ring. Regions 2 and 3: zones where H is out of region 1
but may interact with the π-ring. Unless otherwise noted, the program was run to search forshort H/π contacts with the following conditions: Dmax = 3.05 Å; Dpln < Dmax (region 1); Dlin <Dmax (region 2); Datm < Dmax (region 3); max = 127.5°, -max <  < max;  < 63°. Dhpi: H/
distance (Dpln for region 1, Dlin for region 2, Datm for region 3).

179

3.9.2.

Edit parameter

The dialog is shown in Fig3.72. Specify input parameters.

Fig3.72 Input parameter dialog
It explains the behavior of File menu.
1) OpenOpen parameter file and those parameters is set in GUI. The file that specified at
Pi-system loaded and set PI Information tab.
2) Save
Save parameters.
3) Set Default Value
Set default value. PDB File set displayed file at 3D view. Pi-system Table is set as“PDB filename.vpi”, and if this file exists load this file as PI Information. If this filedose not exist, default value is set.
4) Close
Close the dialog.

180

It explains input parameters.
1) PDB File
Specify the PDB file to be analyzed.
2) Pi-system Table
Specify the PI information file. By clicking the Edit button, PI Information dialog is
popup.
3) H/pi interactions
Specify the output file.
4) Co-ord. of H/pi interaction atom
Specify the coordinate file.
5) Residue & atom to delete[A7]Specify the atom and residue name that dose not analyzed. Please input ”END” atlast line.
6) Distance from hydrogen to pi center
Specify the range of distance(Dcent) from H and center of the ring(O). Please do notchange usually.
7) H/pi distance from hydrogen to pi-system
Specify the range of region1(Dmax)
8) OMEGA<127.5(deg), ALPHA(Hangle)<６３(min63~90)(deg)Specify ω and α. Please do not change usually.
9) Type of ALPHA(Hangle):H-X-R
Specify the H-X-R angle [R=pi_plane, line(A1-A2), A1(closest pi_atom)]．Defilt is a).
a) region1~3: R=pi_plane All region use H-X-pi_plane（=α）b) region1: R=pi_plane,region2:R=line,region3: R=A1c) region1~3:R=A1

use H-X-A1 for all region.

10) Type of display for CHpi contacts
Specify contact coordinate on pi planea) region1: pi_plane (Dpln), region2: line (Dlin), region3: A1 (Datm)b) region1~3: A1 (Datm)c) region1~3: O (Dcent)

a)

b)

c)

181

11) Type of interactions
Specify type of interactions. The distinction of inter/intra is distinguished in chain
ID of the PDB file.
12) Type of regions
Specify type of regions.
13) Type of XH(NXATM)
Specify the atom.
14) H-pi network
Specify output H-pi network on/off
15) Execute CHPI Program
Execute CHPI program by clicking this button.

1823.9.3.

Edit PI Information file

Cliking the button of Edit at Pi-system Table, the dialog is popuped. It is shown in
Fig3.73.

Fig3.73 PI Information panel
The file format
 ID unique name Residue name Specify residue name that are in PDB.
 K Specify the component number in residue.
 L Specify the serial number in one component .
 M Specify number of ring element in component at first line only .
 VPI Specify FIV/SIX/OLE
 N Specify number of atom in ring element.
 1-6 Specify atom name in ring element.

183

The example of editing PI information is shown.
Clicking the suitable atom(C18) in 3D view and select Tool→Display Residue inDistance. Specify 10Å at the dialog. Select Tool→Set Rotation Center(Fig3.74). So
displayed around C18 and set center of spinning.
Clicking STU at Tree view by right button on mouse, popup the display attributedialog. Specify Color(Atom) and Model(Stick). (Fig3.75)

Fig3.74 Select “Display Residue in Distance” and “Set Rotation Center”

Fig3.75 Set Model and Color of STU by clicking right button of mouse184

It explains the behavior of each button.
1) Highlight selected atoms in 3D viewer
The selected Atoms in 3d viewer is shown highlighted.

2) Add a atom name that picked in 3D viewer
If you select “On”, insert atom name at cursor position.

185

Explain the File Menu.
1) OpenOpen PI Information file and those parameters is set in GUI.
2) Save
Save PI Information.
3) Set Default Value
Set default value. Information on the fixed form on amino acid, DNA, and RNA isset. Besides, it is set recognizing the ring of the part of HEM of the PDB filespecified with PDB File at Input Data tab. ID is set as XXX. It is generated oneelement

from

some

rings.

The

user

can

edit

it.

The

1qpj_CHminCFFAB.pdb is shown below.

Fig3.76 Default PI information of 1qpj_CHminCFFAB.pdb
4) Close
Close this dialog.

186

exampleof3.9.4.

Execute program

Clicking by the “Execute CHPI Program” button, then to start to execute CHPI programat Command Prompt. The Execute log is shown in it.

Fig3.77 Command prompt of CHPI execution
When end the program, to close the command prompt. Then result is displayed in 3D
view. One interaction is named as CHPIn（n:serial number）, By clicking CHPI on 3Dview, then display distance of this interaction at message area. The example is shown in
Fig3.78, Fig3.79 and Fig3.80.

Fig3.78 Result of CHPI(Click CHPI75)

187

Fig3.79 Change preference (Model : Line Solid, Color : blur)Fig3.80 The residue that is around the ligand displayed by Stick Model.

1883.10. Analysis sample of electron density grid data of the CNS form
It's possible to compare an electron densities of the CNS form the experiment which is
X-ray crystallographic analysis and the electron densities calculated by FMO.

3.10.1. Example of AJF
A check is put in “CNS formmated Electron Density (*.cns)” in a GRIDCNTRL tab of
the ABINIT-MP Input File window (figure 3.81) to output result by the CNS form.
It's necessary to be used the same grid point, to compare experimental data which is
get from X-ray crystallographic and calculate density by ABINIT-MP. When you have a
CNS file of experimental data, the same grid be specified by cliking
button.(Fig3.81)

Fig3.81 GRIDCNTRL tab

189“Import”

3.10.2. An display example of grid data of the CNS form
It's possible to load a file of electron density grid data of the CNS form by drag anddrop's to BioStation Viewer.

Fig3.82 Load grid data and display isosurface for 0.1 e/Å3190

3.10.3. An example : the extracted electron density around protein is used
After load electron density, it's possible to extract data by select “Tool → Extract
Density” menu on Isosurface Value dialog. An example is shown Fig3.84.
You can save extracted data to CNS form file by select “File → Save file” menu.

Fig3.83 GUI to extract electron density(a) experimental data(b) extracted data

Fig3.84 An example of extracted data : Crambin(3NIR) (1.0 Å)

191

3.10.4. Compare grid data
You can compare some grid data numerically by selected “Monitor → Compare
Density Files” menu.
The example of Crambin(3NIR) : compare the experimental data and the calculated
data by (FMO-MP2/6-31G*), electron density which is within 1.0Åfrom ARG10. A
difference of 2 of electron density is shown to 3D screen of Viewer, and display and amean of the absolute value of the difference of electron density(average of abs(Δρ)) isshown to a message panel.
You can save difference data to CNS form file by select “File → Save file” menu.

Fig3.85 The example of Crambin(3NIR) : compare the experimental data and thecalculated data by (FMO-MP2/6-31G*), electron density which is within 1.0Åfrom
ARG10

192

4 Super moleculeThis section describes that the formula of supermolecule calculation.
In case of the supermolecule calculation by FMO Method, the Complex
Fragmentation simply consist of protein and ligand.(C:Complex P:Protein L:Ligand →C= P∪L). Each energy described to Complex total energy : EC、Protein total energy : EP、
Ligand Protein total energy : EL. The Interaction Energy between protein and ligand:Δ
E was given byE  E C  ( E P  E L )(exp 4.1)

Supposing E , E , E were calculated by FMO2, ΔE was given byCPLE  E C  ( E P  E L )


~C 
~P
~L 
P
L
  E '   EIJ    E 'I   EIJ   E 'I   EIJ 
I
I J
I J
I
I J
I

I C
I , J C
I , J PI L
I , J L
 I P
C
I(exp 4.2)( E ' : Monomer energy excluding contribution from environmental electrostatic potential,~
E IJ : Inter-fragment interaction energy） If E C is decomposed into the term that innerprotein, inner lgand and intermolecule protein-ligand,~~~E C   E 'CI   E IJC  E 'CI   E IJC  E IJC
I J
I , J P

I
I P

I J
I , J LI
I L

(exp 4.3)

IJ
I P J L

and pack terms of protein and ligand.

EI  EIC  EI P

I P EI  EI

I L

C

L

(exp 4.4)~
EIJ is calcutated as bellow,~~~
EIJ  EIJC  EIJP~~ EIJC  EIJL

I, J  P
I, J  L

193(exp 4.5)

ΔE is given by


 


~  
~ 
~


E    EI   EIJ     EI   EIJ    EIJC
I J
I J
I
 I
 I J
I , J P
I , J L
 I P  I L
 I P J L

(exp 4.6)

The first term is stabilization energy by electronic relaxation of protein that given bybinding protein and ligand. The second term is stabilization energy by electronic
relaxation of ligand. The third term is IFIE of between protein and ligand.
In Viewer, read each CPFs(complex, protein and ligand), and specified corresponding
fragmentation number in that.
Next describes the concrete calculation method which calculates super molecule value
from IFIE and momomer value.
1) Step１ calculation of E'I
Subtract complex from protein and ligand at monomer value.

 EI
'

C

P

―
L

図 4.1


Memory image of EIJ~

2) Step２ calculation of EIJ
Subtract complex from protein and ligand at IFIECP～ E IJ―
L

194

図 4.23) Step3~

Memory image of EIJ~C 'calculation of Supermolecule IFIE EIJ

Calculate Supermolecule IFIE using Step1 and Step2 results.
Protein ： EI  EI 

1
~
EIK

2 K I(exp 4.7)

K P

Logand： E J  E J 

1~
E JK
2 KJ(exp 4.8)

K L

~
~
E IJC   E IJC  E I / J  E J / I(exp 4.9)～

 E IJ～

  E

K I
K P

IJ

I

～

J

図 4.3

Memory image of  E JK

KJ
K L

~

 E

IJ

Each half of the changed portion of IFIE values by electronic relaxation inner protein isrestored to each fragmentation at the second term of (exp 5.7). The ligand is the same at(exp 5.8).
The Protein – ligand IFIE analysis that regards the effect of the electronic relaxation byprotien – ligand binding in fragment unit becomes possible by this calculation result.

195

5 Option of optimize structure
The Structure optimization is executed by calling another program from Viewer. Here,the option that can be specified is shown below. The file that describes this option isprepared, and it specifies it on the screen of the structure optimization.
Hydrogenationofprotein (arbitrariness)-B
The calculation of Atom type is specified.
-nSpecificationofstructure optimization(arbitrariness)

Addition of hydrogen atom (When -B is specified, it is effective).
When you add hydrogen : No filling in
When you do not add hydrogen : -n-O
Execution of structure optimization by XUFF force field.
When you do the structure optimization calculation : -O
When you do not do the structure optimization calculation: No filling in-X #The optimization calculation loop interval of the charge
recalculation by the MQEq method (when -O is specified, it iseffective) is specified by positive integer #.
-hOptimization of atomic site of hydrogen (when -O is specified, it iseffective). It is assumed that ACTIVE shown by the following was
specified for all the hydrogen atoms and processes it. It is assumed that
INACTIVE shown by the following was specified for all atoms except
the hydrogen atom and processes it.
-S
A heavy atomic location of a main chain is fixed. Optimization of side
chain structure and atomic site of hydrogen (when -O is specified, it
is effective). It is assumed that ACTIVE shown by the following was
specified for all atoms except a heavy atom of a main chain andprocesses it. It is assumed that INACTIVE shown by the following was
specified for all heavy atoms of a main chain and processes it.
The method of recognizing a main chain in the PDB form and the
MOL2 form is as follows.
Main chain of PDB form :Atom name
N
CA
C
O
OXT

196

Main chain of MOL2 form :Atom nameAtom typeN
N.4 或いは N.am
CA
C.3
C
C.2
O
O.2
OXT
O.3
(The one to fill both)-T
Processing of N end and C end.
When you dissociate N end and C end : -T
(NH4+, COO-)
When you dissociate neither N end nor C end : No filling in(NH3, COOH)-R
Processing ASP, GLU, LYS and ARG.
When you specify the charge state : -R
When you specify the state of the neutral : No filling in-H #Processing of imidazole ring of histidine (Default is π type).
π type (d type) : -H dτ type (e type) : -H eｐ type (p type) : -H p
-C # cAll charges of each molecule are specified.
# : Number of moleculec : charge
In default, all charges of each molecule are zero.
The method of distinguishing the molecule in the PDB form and the
MOL2 form is as follows.
Distinction of molecule of PDB form : (Uncorrespondence of part)
It confirms it in order of TER, HETATM, a molecular name (residuename), and the residue number. In the following cases, the molecule
is changed.
・ When TER appears.
・ When HETATM appears.
・ When a molecular name in HETATM is changed (A moleculethat is smaller than about five atoms is excluded. The watermolecule is excluded.).
・ When changing from HETATM into ATOM.

197

・ When the residue number becomes small
Distinction of main chain of MOL2 form :Information on following Substract id and Substract name is usedand distinguished.
Substract id : Given integer of amino-acid residue and each low
molecular weight compound. It is counted inascending order.
Substract name : Name of amino-acid residue and compound. Even
when Substract id is not changed, this Substract
name is changed if a different low molecularweight compound is continuously specified.
-k [Tinker_key_file] : The Keyword Control file of the Tinker form is
specified (When -O is specified, it is effective.).
The default name is tinker.key.
Whether each atom is ACTIVE or INACTIVE can be specified.
Example) ACTIVE 4 -9 17 23
When atoms 4, 9-17, and 23 are calculated, it is activated. Minus(-) means the start of the range. Two or more ACTIVE can be
specified. Two or more INACTIVE can be still specified in themeaning opposite to actively. However, when the same atoms
are specified for both ACTIVE and INACTIVE, it becomes
ACTIVE. The atom not specified even for any ACTIVE andINACTIVE becomes ACTIVE.
-f [xuffopt_parameter_file][xuffopt_parameter_file] : The file of the parameter of xuffopt
original form is specified. Options other than -f, the following total
conditions ACTIVE_RESIDUE, INACTIVE_RESIDUE and
ACTIVE_SIDECHAIN concerning the amino-acid residue, andconditions SDLOOP, CGLOOP, MAXLOOP, SDGRADIENT,CGGRADIENT, RENERGY and RGRADIENT concerning theconvergent calculation of the optimization loop can be specified.
The default name is xuffopt.par.
Whether each amino-acid residue is ACTIVE_RESIDUE or
INACTIVE_RESIDUE can be specified. The specification method is
the same as ACTIVE and INACTIVE.
Example) ACTIVE_RESIDUE 4 -9 17 23
When residue 4, 9-17, and 23 are calculated, it is activated.
Minus (-) means the start of the range. Two or more
ACTIV_RESIDUE can be specified. Two or more
INACTIVE_RESIDUE can be still specified in the meaning
opposite to actively. However, when same residue are specified
for both ACTIVE_RESIDUE and INACTIVE_RESIDUE, it
becomes ACTIVE_RESIDUE. The residue not specified evenfor any ACTIVE_RESIDUE and INACTIVE_RESIDUE

198

becomes ACTIVE_RESIDUE.
ACTIVE_SIDECHAIN can be specified for the side chain ofeach amino-acid residue (parts except a main chain). The
specification method is the same as ACTIVE and
ACTIVE_RESIDUE.
The settling calculation frequency and the settling judgment conditionof the optimization loop can be specified (The following examples are
the default values).
Example)SDLOOP 100
CGLOOP 400
MAXLOOP 500
SDGRADIENT 1000.0
CGGRADIENT 0.1
RGRADIENT 0.1
RENERGY 0.0001
SDLOOP : Number of maximum Steepest Descent law loops(SD loop)
CGLOOP : Number of maximum Conjugate Gradient law loops(CG loop)
LOOPMAX : Number of maximum loops
SDGRADIENT : Gradient discontinuance value of SD loop
CGGRADIENT : Gradient discontinuance value of CG loop
RGRADIENT : Tolerance for convergence of Gradient
RENERGY : Tolerance for convergence of rest error (kcal/mol) of
all energy
Gradient is judged by the value of the second power harmony route.
The unit is (kcal/mol･Å). The CG loop continues to "Number ofmaximum SD loops + number of maximum CG loops" when the SD
loop is discontinued on the way.
Because the BFGC method is not being calculated now, CGLOOP
and CGGRADIENT are invalid.

199

6 Installation
6.1 Distribution
We have a windows installer file.
6.2 System Installation
Double-clicking install file icon then installs it. To execute the viewer by selecting menu
that is start→ABINIT-MP Open Consortium→BioStationViewer.
The wroking folder is install folder. You can change it to change property of menu item
and add a install path to PATH like bellow.
C:¥Program Files¥ ABINIT-MP Open Consortium ¥BioStationViewer
6.3 System Requirements
System Requirements is shown in Table 7.1.
Table 6.1 System Requirements
Item

Business

OS

Windows(2000/XP,7)CPU

Pentium Ⅱ 400MHz or more

MemoryRecommended memory 2GB or more

6.4 File Acquisition
Obtain Biostation Viewer files from a web site of ABINIT-MP. The following files needs
to run Biostation Viewer.
File name
Explanation
BioStationViewerOpen_1.0_rev25.exe BioStation Installer filesampleData.zip

Sample files

tutrial.zip

Tutorial data files

6.5 Reduce
You can use Reduce in order to add hydrogen.

Reduce can be downloaded fromhttp://kinemage.biochem.duke.edu/software/software2.html#reduce, which is a program free of charge.
Download the program and save it to the appropriate place. Set Path to the folder,then. Refer to the preceding paragraph so as to set Path. Options are shown as
follows.
reduce: version 2.15 10/4/01, Copyright 1997-2001, J. Michael Word200

arguments: [-flags] filename or Adds hydrogens to a PDB format file and writes to standard output.
(note: By default, HIS sidechain NH protons are not added. See -BUILD)
Flags:-Trim

remove (rather than add) hydrogens-NOOH

remove hydrogens on OH and SH groups-OH

add hydrogen on OH and SH groups (default)-HIS

create NH hydrogen on HIS rings-FLIPsallow complete ASN, GLN and HIS side chains to flip
(usually used with -HIS)-NOHETh

do not attempt to add NH proton on Het groups-ROTNH3

allow lysine NH3 to rotate (default)-NOROTNH3

do not allow lysine NH3 to rotate-ROTEXist

allow existing rotatable groups (OH, SH, Met-CH3) to rotate-ROTEXOH

allow existing OH & SH groups to rotate-ALLMEthyls

allow all methyl groups to rotate-ONLYA

only adjust 'A' conformations (default)-ALLALTprocess adjustments for all conformations-NOROTMET

do not rotate methionine methyl groups-NOADJust

do not process any rot or flip adjustments-BUILD

add H, including His sc NH, then rotate and flip groups(except for pre-existing methionine methyl hydrogens)(same as: -OH -ROTEXOH -HIS -FLIP)-Keep

keep bond lengths as found-NBonds#

remove dots if cause within n bonds (default=3)-Model#which model to process (default=1)-Nterm#max number of nterm residue (default=1)-DENSity#.#

dot density (in dots/A^2) for VDW calculations (default=16)-RADius#.#probe radius (in A) for VDW calculations (default=0)-OCCcuttoff#.#

occupancy cutoff for adjustments (default=0.01)

201

-H2OBcuttoff#.#

B-factor cutoff for water atoms (default=40)-H2OOCCcuttoff#.# occupancy cutoff for water atoms (default=0.66)-PENalty#.#

fraction of std. bias towards original orientation (default=1)-HBREGcuttoff#.# over this gap regular HBonds bump (default=0.6)-HBCHargedcut#.# over this gap charged HBonds bump (default=0.4)-BADBumpcut#.#

at this gap a bump is 'bad' (default=0.4)-SEGIDmap "seg,c..." specify chainID based on segment identifier field-Xploruse Xplor conventions for naming polar hydrogens-NOCondrop connect records-LIMIT#max num iter. for exhaustive search (default=100000)-NOTICKs

do not display the set orientation ticker during processing-SHOWSCore

display scores for each orientation considered during processing-FIX "filename"if given, file specifies orientations for adjustable groups-DB "filename"file to search for het info
(default="/usr/local/reduce_het_dict.txt")

note: can also redirect with unix environment variable: REDUCE_HET_DICT-Quietdo not write extra info to the console-REFerence

display citation reference-Helpmore extensive description of command line arguments

6.6 Babel
Set BABEL_DIR(Environment Parameter)
C:¥Program Files¥ ABINIT-MP Open Consortium ¥BioStationViewer¥babel-lis

202

6.7 Bond Builder
The use of “bond_builder” which is the hydrogenation program is shown in Table 6.2.

Table 6.2 Explanation of the use of “bond_builder”.
Command line

Setting of the input file

Setting of the output fileHydrogenation of protein(arbitrariness)

Processing of N terminal
and C terminal of theprotein(arbitrariness)
Processing of charged
residues ASP, GLU,
LYS and ARG(arbitrariness)
Processing of imidazole
ring of histidine(Default is π type)% bond_builder.exe –i [input_file_name] [input_file_type]–o [output_file_name] [output_file_type]–B –n –T –R –H #–i [input_file_name] [input_file_type][input_file_name] : Input file name (indispensable).
[input_file_type] : Type of the input file (arbitrariness).
pdb, ent : For the type of PDB
mol2 : For the type of mol2
Default file type is decided by the extension of the input file name. Filetype is PDB in the case of pdb or ent , and mol2 in the case of mol2.
–o [output_file_name] [output_file_type][output_file_name] : Output file name.
[output_file_type] : Type of the output file (arbitrariness).
pdb, ent : For the type of PDB
mol2 : For the type of MOL2
Default file type is decided by the extension of the output file name.
File type is PDB in the case of pdb or ent , and mol2 in the case ofmol2.
When “－o” is not specified, the file name that adds “_builder” to the
input file name is output. example) input_builder.mol2
At this time (“-o” is not specified), when “-B” (see below) is specified,
the file name that adds “_H” to the input file name is output. example)
input_H.pdb–B
The calculation of Atom type is specified.
–nAddition of hydrogen atom (When -B is specified, it is effective).
When you add hydrogen : No filling in
When you do not add hydrogen : -n–T
When you dissociate N terminal and C terminal : -T
(NH4+, COO-)
When you dissociate neither N terminal nor C terminal : No filling in(NH3, COOH)–R
When you specify the charge state : -R
When you specify the state of the neutral : No filling in–H #π type (d type) : -H dτ type (e type) : -H eｐ type (p type) : -H p

203

6.8 TINKER
Download from http://dasher.wustl.edu/tinker/, and add Path (install folder/bin). Copy

install folder/ｊre/bin/client/jvm.dll to bin.

204

7 Acknowledgement
We refere the following projects.
Information-Technology Promotion Agency, Japan(IPA)“Research of protein functional prediction system for biotechnology industry”“Development of ab initio fragment molecular orbital method program: ABINIT-MP”

Japan Science and Technology Corporation
Research and Development for Applying Advanced Computational Science andTechnology
Ab initio Approach to Nanoscale Dynamics of DNA

This work was supported the following projects.
Ministry of Education, Culture, Sports, Science and Technology
Frontier Simulation for Industrial Science” Quantum Molecular Interaction Analysis”



The Japan Science and Technology Agency
Core Research for Evolutional Science and Technology(CREST)
Development of Bio-Simulation Systems Based on the Fragment Molecular Orbital
Method

Ministry of Education, Culture, Sports, Science and Technology
Revolutionary Simulation Software for 21st Century (RSS21)



Ministry of Education, Culture, Sports, Science and Technology
Research and Development of Innovative Simulation Software (RISS)MOLDA is developed by Dr. Hiroshi Yoshida. Sad to say he was lost in 2005. He was amember of our CREST project, so he gave us a permission to use the MOLDA.
Eigenvalue are required to evaluate in the calculation, with using JAMA;Java Matrix
Package (http://math.nist.gov/javanumerics/jama/). JAMA is operating free of charge.

205

We are deeply grateful to following people.
Kobe University Dr. Sigenori Tanaka, Dr. Ikuo Kurisaki
Rikkyou University

Dr. Yuji Mochizuki

Kagoshima University Dr. Takeshi, Ishikawa
MOLSIS Inc. Dr. Shinji Amari
Hiroshima University
Advance Soft co.

Dr. Hiroshi Yoshida

Dr. Tetsuji Ogawa, Dr. Masato Kobayashi

Advanced Industrial Science and Technology Dr. Yuto Komeiji, Dr. Kazuo
KitauraMicrobial Chemistory Research Center Dr. Yuji Umezawa
The CHPI Institute Dr. Motihiro Nishio
Hoshi University Dr. Kaori Fukuzawa
National Institute of Health Sciences Dr. Tatsuya Nakano, Dr. Yoshio Okiyama.
RIKEN Dr. Chiduru Watanabe
Mizuho Information & Research Institute, Inc. Kouichuro Kato, Takashi
Tsukamoto, Naoki Tanimura
Scorpion Tech LLC. Akifumi KatoFMODD Consortium（In random order）

206

8 References
FMO
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2.

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edited by D. G. Fedorov and K. Kitaura “The Fragment Molecular Orbital Method:
Practical Applications to Large Molecular Systems”

Taylor & Francis/ CRC Press, Boca

Raton, FL, (2009)

FMO Structure Optimize(Differential)
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163-170 (2001).

FMO-MD
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Y. Komeiji, T. Nakano, K. Fukuzawa, Y. Ueno, Y. Inadomi, T. Nemoto, M. Uebayasi,
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Y. Mochizuki, Y. Komeiji, T. Ishikawa, T. Nakano, H. Yamataka “A fully quantum
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CIS(D)
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VISCANA
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Comp. Chem., 27, 948-960 (2006).
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CH/π
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アドバンスソフト

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BioStation Viewer
33. 加藤、福澤、望月、甘利、中野 「BioStation Viewer：生体高分子の相互作用も解析と可視化」可視化情報

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34. Wolfgang Kabsch and Christian Sander ,"Dictionary of Protein
Secondary Structure: Pattern Recognition of Hydrogen-Bonded andGeometical Features", Biopolymers, Vol. 22, 2577-2637, 1983.

Appendix1) ABINIT-MP File Format : another file2) MOLDA users manual : another file210