Subject: Simple program for editing protein structure

From: Bjoern Rabenstein <[email-masked]>
Date: Thu, 13 Jan 2000 19:39:31 +0100

Hi CCLers!

I'm just wondering if out there is any small and simple program to
interactively manipulate protein (or any large molecular) structures. It
would already be sufficient to modify dihedrals and at the same time watch
what's happening.

I know that this is possible with huge (and expensive...) program packages
like InsightII or Quanta, but I think that's not really the main feature
of these programs, and I'm not willing to buy a lot of great features I
don't want.

It would be just nice to quickly load a small programm (best for Unix, so
that I don't need to run to the secretary's office or reboot the PC... :-)
to change these one or two dihedral angles in my PDB file such that there
will be no clashes.

After all searching so far I've only found tons of sophisticated viewing
programs, but no interactive manipulation programs except as subfeatures
of large molecular modelling packages or as molecule builders of quantum
chemical programs (which are not suitable for really large molecules).

Thanks for any hints!
-- 
Bjoern Rabenstein * PhD student * Freie Universitaet Berlin * Fachbereich
Biologie/Chemie/Pharmazie * Inst. f. Chemie * Takustr. 6 * D-14195 Berlin
[email] [email-masked]                  [phone] +49-30-838-3484
[WWW] http://userpage.chemie.fu-berlin.de/~rabe/    [fax] +49-30-838-3464

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From: "Richard P. Muller" <[email-masked]>
Date: Thu, 13 Jan 2000 11:40:32 -0800

> would already be sufficient to modify dihedrals and at the same time watch

Konrad Hinsen's program suite Molecular Modeling Tool Kit (MMTK) is a
very useful tool for doing this type of work. It requires some knowledge
of the Python programming language (which isn't all that difficult).

http://starship.python.net/crew/hinsen/MMTK/

There are a number of viewers that are associated with it

There is also a good mailing list supporting the project, and Konrad
himself is quite helpful should a problem arise.

The other advantage to MMTK over a package is that since you have the
source code, if it doesn't do everything you like, you can modify it to
do what you want.

Rick

-- 
Richard P. Muller, Ph.D. 
[email-masked] 
http://www.wag.caltech.edu/home/rpm

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From: Rick Venable <[email-masked]>
Date: Thu, 13 Jan 2000 14:43:40 -0500 (EST)

One of the more useful simple tools I've found for this is a custom
version of Rasmol, from the UC Berkely Chem. Dept.; there are MacOS and
Wintel versions of executable programs.  The URL is:

	http://mc2.CChem.Berkeley.EDU/Rasmol/

The major changes vs. the standard Rasmol are:

- ability to load more than one molecule
- ability to rotate torsions and change conformations

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]          |    \  /  |=|    position of the FDA; for that,
http://www.erols.com/rvenable       \/   |=|    see   http://www.fda.gov  )