How to display 3D structure of PDB files with a PC?
danj at welchgate.welch.jhu.edu
Tue Dec 29 12:05:48 EST 1992
In article <92360.094143U59918 at uicvm.uic.edu> Dong Li 312-996-0509 <U59918 at uicvm.uic.edu> writes:
>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.
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.
danj at 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 (220.127.116.11) 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 ;-)
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 :)
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 at 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.
Dr. Ferenc Czegledy writes:
There are several ways that I know of to visualize PDB files in the MS-DOS
>>>1. Using pdViewer which one can obtained by anonymous ftp from
>>>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
630 W 168th Street
New York, NY 10032
email: ferenc at 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.
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 at krsnucc1.BITNET
Eric R. Hugo, Postdoctoral Research Associate |eric at bcserv.wustl.edu
Dept. of Biochemistry and Molecular Biophysics|
Washington University School of Medicine |
Box 8231, St. Louis, MO 63110_________________| (314) 362-3342
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