Subject: Summary: Simple program for editing protein structure

From: Bjoern Rabenstein <[email-masked]>
Date: Wed, 09 Feb 2000 18:55:25 +0100

Dear CCLers!

A little bit late, but here it is:

I asked for simple and cheap programs for interactively editing protein
structure on a low level (e.g. modifying torsion angles, but not doing
mutations).

There are a lot of programs that do what I want. Of course, most of them
do a lot more. However, there is no ideal case (does what I need && free
&& open source && runs without problems or limitations)...

The free part:

- SWISS-PDBVIEWER: no source, binaries available for IRIX, Linux, 
  MacOS and "PC" (which probably means Windows :)
  http://www.expasy.ch/spdbv/
  (thanks to Osmar Norberto de Souza <[email-masked]> and Nick Rhodes
  <[email-masked]>)

- ICMLITE: only the "lite" version is free, no source, available for 
  IRIX, Win95/NT, Linux (Intel + PPC) Dec-Unix, Solaris
  I could not try the program since I got the following error message;
    can't resolve symbol '__register_frame_info' 
  (even if I preload a special libregframe.so supposed to fix this)
  http://www.molsoft.com/
  (thanks to Renxiao Wang <[email-masked]>)

- MODIFIED RASMOL: a enhanced version of RasMol based on the old
  version 2.6. No source, Binaries fo MacOS, "PC" (s.o.), Linux, DEC-Unix
  HP-UX, -->>Unix-versions for 8bit display only<<--
  http://mc2.CChem.Berkeley.EDU/Rasmol/
  (thanks to Rick Venable <[email-masked]>)

- MOILVIEW:  with source, but it uses SGI-GL, so it will
  only compile on SGI machines and some IBM RS/6000.
  http://morita.chem.sunysb.edu/~carlos/moil-view.html
  (thanks to Carlos Simmerling <[email-masked]>)

- MOLDEN: This is more suitable for small molecules. With
  large molecules like proteins, it is very slow.
  http://www.cmbi.kun.nl/~schaft/molden/pdb3.html
  (thanks to Gijs Schaftenaar <[email-masked]>)

The expensive part:

- MIDAS: academic license $350.
  http://www.cgl.ucsf.edu/Outreach/midasplus/
  (thanks to Jeffrey P. Jones, [email-masked])

- COSMOS: only available for Windows, academic about DM 1000 ($500).
  http://www.cosmos-software.de/
  (this we already knew by ourselves)

Two of you gave me the following hint, but I'm not sure, if this is what I
wanted:

- MMTK: I was already aware of this free and open source toolkit of Konrad
  Hinsen. But as far as I have understood, it is suitable to modify a
  molecular structure by scripts. Indeed, this is what I do usually,
  but this time I needed a tool to rotate a part of a molecule and watch
  it moving (to say "stop!" at the right moment). Perhaps such a tool 
  could easily be assembled using MMTK, but I don't know if anybody has
  already done it.
  http://dirac.cnrs-orleans.fr/MMTK/
  (thanks to Konrad Hinsen <[email-masked]> and Richard P. Muller
  <[email-masked]>)

Thanks again for all the hints!
-- 
Bjoern Rabenstein * PhD student * Freie Universitaet Berlin * Fachbereich
Biologie/Chemie/Pharmazie * Inst. f. Chemie * Takustr. 6 * D-14195 Berlin
[email] [email-masked]                 [phone] +49-30-838-53484
[WWW] http://lie.chemie.fu-berlin.de/~rabe/        [fax] +49-30-838-53464