[MMTK] protein setup

D. Joe Anderson deejoe@iastate.edu
Fri, 16 May 2003 14:24:03 -0500


On Fri, May 16, 2003 at 02:26:56PM +0200, Jaroslaw Kalinowski wrote:

> As I understand, the question below should be considered as a "feature
> request" - in some programs there are builders that allow to assemble,
> for example, helices or beta-strands given only the sequence. I also
> think that it would be nice to have buildHelixFromString(["Ala", "Gly",
> "Tyr", ...]). 
> Unfortunately I don't know of any module that would do this...

A module seems to be overkill for the regular secondary structure--this is
something that can be scripted with various tools.

The last time I've done this was in MOLMOL.  MOLMOL lacks control
structures, so iterating over a range of residues has to be done some other
way, but using Perl to spit out the MOLMOL commands to build the chain and
then to set the backbone torsion angles was straightforward.

I would be very surprised if the same approach wasn't available using Python
with either mmtk or pymol.

--Joe
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D. Joe Anderson, Asst. Sci.       Computing Support for Botany, ZG, & BBMB.
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