[MMTK] protein setup

Konrad Hinsen hinsen@cnrs-orleans.fr
Sat, 17 May 2003 22:44:37 +0200


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

A Python module is no more effort to write than a Python script!

> structures, so iterating over a range of residues has to be done some o=
ther
> 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.

Sure, yes, in principle. But I see such kludges as clearly outdated. My g=
oal=20
with MMTK has always been to provide an integrated environment for=20
everything. If external programs are involved, then they should be wrappe=
d up=20
to make this "implementation detail" transparent to the user as much as=20
possible. For an example, see how PDB viewers are integrated into MMTK.

Konrad.
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