From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Re: How to display 3D structure of PDB files with a PC?
Organization: Johns Hopkins Univ. Welch Medical Library
Date: Tue, 29 Dec 1992 17:05:48 GMT

In article <92360.094143U59918@uicvm.uic.edu> Dong Li 312-996-0509 <U59918@uicvm.uic.edu> writes:
>Dear Netters,
>
>I am trying to do the tertiary modeling now. I will be very grateful
>if you tell me how I can get a program to display with an IBM PC
>the tertiary or stereo structures of the proteins, based on the
>data files from Brookhaven Protein Database.
>
>Any help will be appreciated very much.
>
>By the way, thanks a lot to those who helped me previously.
>Due to the uncertain network problem, I failed to reply and say THANK YOU
>to some of them.
>
>Dong Li

*****************************************************************************

There was a discussion about this last summer as well as a followup earlier 
this month - there are pros and cons to using a PC for this type of work - 
much depends on what you want to do (but that's another discussion :-).

Eric Hugo of Wash U. St. Louis posted the follwoing summary about the responses
to his (similar) question.  


Regards,


Dan Jacobson

danj@welchgate.welch.jhu.edu

================================================================================


     Of the answers I received one set of programs was mentioned that is
available by anonymous ftp.  These are shareware programs written at the
University of Illinois and distributed by Dr. A.R Croft.  These
programs (pdViewer and PSAAM) are written in Visual Basic and run
under Windows 3.x.  I've just downloaded them and am in the process of
evaluating them.  The two programs can be obtained from
nemo.life.uiuc.edu (128.174.183.6) in the pub/pdvwin and the pub/psaam
subdirectories by anonymous ftp.
     Thanks to all of the individuals that responded to my query, the
information was greatly appreciated.      Eric  ;-)

SUMMARY INFORMATION:


Tom Branham writes:

I do know of a commercial program called HyperChem from Autodesk
for which the educational price is $600, but they do have a full
free to researchers program (if you keep them updated on your work, etc.)
The program is not only a visual interface, but performs molecular
orbital calculations and molecular dynamics.  I have been very tempted
to take them up on the research program, but the one thing worrying me
is that it comes with a hardware key and I have serial ports that are not
well behaved.  If anyone else comes up with any other sugestions I
would appreciate hearing about them, as I am running Quanta at the lab,
on our SGI's, and then I am working with my own programs, lotus123 and
Mathcad at home on the pdb files, but can not view them at home, a minor
irritation.  I also purchase the programs on my own rather than with
lab moneys.  I like to feel that I do not "live off " the lab grants,
perhaps a sense of hubris I REally can not afford this month :)

                            ........Tom Branham
P. S. Dr. Pochapsky brought back the PDB and Atlas of sequences from
      the same meeting.  Wasn't that a Nice suprise.....?


Watson Ko writes:

Alchemy III will do the job you want, but it will be very slow if you try to
rotate(or whatever) since the program has to redraw the whole molecule.

What I did was just showing the active site of the specific enzyme(or
protein) and manipulated the molecule.

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Watson Ko                                   v999r36x@ubvms.cc.buffalo.edu
Space, the final ... parking place!
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Jim Cassatt writes:


I have been using a shareware version of PCMODEL.  Check previous
messages regarding availability.  Included are two sample files
for chymotrypsin and B-DNA obtained from the PDB.  They can be
viewed quite effectively with a 486, less so with a 386SX and
poorly with an 8088.  What I have not been able to find out is
whether a program to convert PDB format to PCMODEL format is
available.  The main difficulty is generating a connect table.

There are also two versions of PCMODET, one a shareware version
and the other distributed by Gilbert at Indiana.  His version
does not have a conversion program.  I awaiting a response from
the author of the shareware program.

Jim Cassatt


Dr. Ferenc Czegledy writes:

There are several ways that I know of to visualize PDB files in the MS-DOS
environment:
>>>1. Using pdViewer which one can obtained by anonymous ftp from
   >>>nemo.life.uiuc.edu
   >>>The package must be transferred using the binary protocol and runs
   >>>under Windows 3.1/3.0.

2. Using a package called Alchemy III (for Windows) which is available
   from Tripos Assoc. Inc. ,St. Louis, MO.  Phone: 314-647-1099.

3. Using Chem-X from Chemical Design Inc., 200 Route 17 South, Suite
   120, Mahwah, NJ 07430. phone: 201-529-3323. I have only seen the
   brochure for this package but it looks very impressive.  The only
   problem is that it is very expensive: ~ $ 2,500.00/year.  The
   software will self-destruct after 1 year but if you pay for an
   additional year the software is upgraded for you.

Anyway, good luck and tell me if you hear of any additional approaches to
visualization and modeling on the PC.
-- Ferenc Czegledy
   Dept. Of Cardiology
   Columbia University
   630 W 168th Street
   New York, NY 10032
email: ferenc@cucrd0.med.columbia.edu


Rhee Hwan-Seok writes concerning the program MOBY

The following is the snail-mail address of MOBY manufacturer.
In my address file they have no e-mail address known.
----------------------------
Springer-Verlag
Heidelberger Platz 3
W-1000   Berlin 33
F.R.G  ( Germany )

Telex : 461723
Telefax : (06221)413982
----------------------------
They will send you a demo disk FREE of charge.
And the disk could be 3" or 5" on your request.

e-mail : hyunerho@krsnucc1.BITNET
-- 
  Eric R. Hugo, Postdoctoral Research Associate |eric@bcserv.wustl.edu
  Dept. of Biochemistry and Molecular Biophysics|                
  Washington University School of Medicine      |               
  Box 8231, St. Louis, MO 63110_________________| (314) 362-3342