| .TH DMS 1 "" "\fBAPPENDIX 6\fP" "\fBUCSF MidasPlus\fP" | |
| .iX zd start | |
| .SH NAME | |
| dms \- calculate a solvent-accessible molecular surface | |
| .SH SYNOPSIS | |
| .B dms | |
| \fIfile\fR [ | |
| .B \-a | |
| ] [ | |
| .B \-d | |
| \fIdensity\fR] [ | |
| .B \-g | |
| \fIfile\fR] [ | |
| .B \-i | |
| \fIfile\fR] [\fB\-n\fR] [\fB\-w | |
| \fIradius\fR] [\fB\-v\fR] \fB\-o\fI file\fR | |
| .SH DESCRIPTION | |
| .I Dms | |
| calculates the molecular surface of a molecule. | |
| The molecular surface resembles the van der Waals | |
| surface of a molecule, | |
| except that crevices between atoms are smoothed over | |
| and interstices too small | |
| to accommodate the probe are eliminated. | |
| The surface includes cavities in the interior | |
| of the molecule, | |
| even if they are not accessible to a solvent molecule | |
| coming from the outside. | |
| .LP | |
| The molecular surface | |
| calculated is that defined by | |
| F. M. Richards (1977, | |
| .I "Ann. Rev. Biophys. Bioeng." | |
| ). | |
| In particular, | |
| the calculated molecular surface is that traced out by the \fIsurface\fP | |
| of the probe sphere rather that the probe sphere's \fIcenter\fP. | |
| According to Richards' definition | |
| the molecular surface consists of two parts: | |
| .I "contact surface" | |
| and | |
| .I "reentrant surface." | |
| The contact surface is | |
| made up of | |
| ``those parts of the molecular van der Waals | |
| surface that can actually be in contact | |
| with the surface of the probe.'' | |
| The reentrant surface is defined by | |
| ``the interior-facing part of the probe | |
| when it is simultaneously | |
| in contact with more than one atom.'' | |
| .I Dms | |
| reports the amounts of contact and reentrant surface area, | |
| and the combined total surface area on the standard error output | |
| (see the \fB\-g\fP flag below). | |
| .LP | |
| .I File | |
| is an input file of coordinates. | |
| The input file must be in the Protein Data Bank format. | |
| The first letter or first two letters | |
| of the atom name is used | |
| to determine the element type. | |
| By default, implicit hydrogens are | |
| included for carbon, | |
| nitrogen and oxygen atoms, | |
| thus aromatic carbons | |
| and nitrogens | |
| will have van der Waals radii | |
| that are somewhat too big. | |
| Note that | |
| only amino acid and nucleic acid residues | |
| will be included unless \fB\-a\fR is also specified. | |
| .LP | |
| .SL | |
| .I Dms | |
| can be set up to run on multiple machines | |
| simultaneously for increased performance. | |
| By default, it only runs on the local host. | |
| The | |
| .SM UCSF | |
| MidasPlus Installation Guide | |
| that came with the MidasPlus | |
| .SM CD-ROM | |
| contains instructions | |
| on how to configure | |
| .I dms | |
| to use multiple machines. | |
| .EL | |
| .LP | |
| .SL | |
| If it is desired to simply visualize a small molecular surface | |
| from within | |
| .SM MIDAS\c | |
| , it may be easier to use the \fImakems\fP(1) delegate, | |
| rather than run \fIdms\fP directly. | |
| Consult the \fImakems\fP manual page for further details. | |
| .EL | |
| .SH OPTIONS | |
| The flags may be in any order. | |
| The meanings of the flags are described below: | |
| .IP \fB\-a\fR | |
| Include all atoms, | |
| not just those in amino acid and nucleic acid residues. | |
| .IP \fB\-d\fR | |
| Change the density of points on the surface. | |
| .I Density | |
| is a factor affecting | |
| the density of points on the surface; | |
| the default of 1.0 produces about 5 points | |
| per square angstrom. | |
| Only values between 0.1 and 10.0 are permitted. | |
| For large proteins, | |
| a density of 0.5 is recommended. | |
| .IP \fB\-g\fR | |
| Write all the informative messages to | |
| .I file, | |
| instead of the standard error output. | |
| Genuine errors still go to the standard error output. | |
| This file is not rewound at any time, | |
| so messages from several runs may be accumulated. | |
| .IP \fB\-i\fR | |
| .iX 36 | |
| Calculate the molecular surface | |
| only for those residues and atoms | |
| specified in | |
| .I file, | |
| but keeping the rest of the molecule | |
| for collision checks. | |
| The file consists of a series of lines | |
| such as the following: | |
| .nf | |
| ASP 205 CA | |
| TYR 13 * | |
| GLY 116 FRM | |
| HIS 178 TO | |
| .fi | |
| .IP | |
| The asterisk means all atoms of the residue | |
| and the ``FRM'' and ``TO'' mean all residues | |
| from 116 to 178 inclusive. | |
| The sequence number may contain letters, | |
| and if the | |
| .SM PDB | |
| input file contains chain identifiers, | |
| then those should be appended on the right of the sequence number. | |
| Residue insertion codes (if any) should be placed between | |
| the sequence number and any chain identifier. | |
| Residues contained in \fCHETATM\fP records should have | |
| an asterisk appended to the end of the residue identifier. | |
| The surface generated using the \fB\-i\fR flag | |
| is not always the same as the surface | |
| generated by running the entire molecule | |
| and afterwards selecting out the desired atoms. | |
| The first surface will not include | |
| reentrant surface lying between | |
| an atom in the \fB\-i\fR file and atoms not in the file. | |
| .iX bd | |
| The | |
| .IR pdb2site (1) | |
| utility may be useful for generating site files. | |
| Consult the | |
| .I pdb2site | |
| manual page for further details. | |
| .IP \fB\-n\fR | |
| Include the unit normals | |
| to the surface with | |
| each surface point record. | |
| .IP \fB\-v\fR | |
| Produce more verbose output. | |
| .I Dms | |
| will announce each computation phase as it is entered | |
| as well as a count of the atom types in the molecule | |
| and the number of computation requests handled by each | |
| host that participated in the | |
| .I dms | |
| calculation. | |
| .IP \fB\-o\fR | |
| The output is written to | |
| .I file. | |
| This flag is not optional. | |
| .IP \fB\-w\fR | |
| Change the water probe radius from the default | |
| radius of 1.4 angstroms. | |
| This parameter must be between | |
| 1.0 and 201.0. | |
| .LP | |
| The output consists of | |
| a series of atom and surface point records, | |
| with the same format for the | |
| first six fields. | |
| Each atom is followed by | |
| the surface points (if any) | |
| which belong to it. | |
| These first six fields | |
| are in the following format: | |
| residue name, | |
| sequence number, | |
| atom name, | |
| x coordinate, | |
| y coordinate, | |
| z coordinate. | |
| For an atom record, | |
| the seventh field is ``A.'' | |
| For a surface point record, | |
| the seventh field begins | |
| with an ``S,'' | |
| followed by a ``C,'' ``R,'' or ``S'' | |
| according to whether | |
| the point is part of | |
| contact, reentrant, or ``saddle'' surface | |
| (``saddle'' is a type of reentrant surface | |
| where the probe is in contact with exactly | |
| two atoms). | |
| This is followed a digit | |
| used for depicting | |
| different density levels. | |
| The eighth field is the | |
| molecular surface area associated | |
| with the point in | |
| square angstroms. | |
| If the \fB\-n\fR flag is specified, | |
| the next three fields are | |
| the unit normal vector | |
| pointing outward from the surface. | |
| Informative messages and errors are | |
| written to the standard error output | |
| unless a \fB\-g\fR file is specified. | |
| .LP | |
| .iX 27 start | |
| The chemical elements and radii | |
| that the program handles are detailed | |
| in the table below. | |
| The program gets these values from the file | |
| .IR /usr/local/midas/resource/dms/radii . | |
| If there is a file in the current directory called | |
| .IR radii , | |
| then | |
| .I dms | |
| will use that file instead. | |
| So in order to add uncommon elements or | |
| use different radii, one should copy the | |
| default file and modify it. | |
| The file format is documented in the file itself. | |
| .sp | |
| .RS 1i | |
| .TS | |
| box; | |
| c c | |
| a n. | |
| Element Radius | |
| _ _ | |
| H 1.20 | |
| C 1.90 | |
| N 1.50 | |
| O 1.40 | |
| F 1.35 | |
| P 1.90 | |
| S 1.85 | |
| Cl 1.8 | |
| Fe 0.64 | |
| Cu 1.28 | |
| Zn 1.38 | |
| Br 1.95 | |
| I 2.15 | |
| Other 1.90 | |
| .TE | |
| .RE | |
| .SH "SEE ALSO" | |
| .SL | |
| pdb2site(1), | |
| The UCSF MidasPlus Installation Guide | |
| .EL | |
| .SH "AUTHOR" | |
| Conrad Huang | |
| .br | |
| University of California, San Francisco | |
| .SH FILES | |
| /usr/local/midas/resource/dms/radii default atomic radii | |
| .iX 27 stop | |
| .br | |
| .SH DIAGNOSTICS | |
| Many and varied. | |
| .iX 37 | |
| Be sure to examine the \fB\-g\fR file before you leave | |
| a background job running overnight. | |
| .iX zd stop | |