-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi David--
> would it be possible with XPLOR-NIH to reduce
> configuration space by refining a C-alpha trace with one degree of
> freedom per residue- torsion angle- and fix all alpha-alpha bond
> lengths, and still use IVM torsion angle dynamics in ensemble mode?
> If so, I'm not certain how to go about this. It looks like I might
> need to generate my own psf. If you think it could work, could you
> outline what steps I might need to take so I can focus on these steps
> in the documentation? Or better, is there an example of something
> similar that you know of and can point me to?
>
you might simply fix all side-chains, leaving only backbone degrees of
freedom.
Do this using something like (assuming dyn is the appropriate IVM object):
from selectTools import getResids
for resid in getResids():
dyn.group("""resid %d and not (name C or name CA or name N or name HN
or name O or name HT# or name OT#)""")
After this, fix omega angles using
torsionTopology(dyn,fixedOmega=True)
then there will be two degrees of freedom per residue.
hope this helps--
Charles
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.3 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/>
iD8DBQFE0mwBPK2zrJwS/lYRAjwhAJ9zq/SQp/Iuw8Pnk6SIFUmhJb4WNQCdFrL+
Vh+JmH/WMQFiAqqmsMHnxT8=
=oazu
-----END PGP SIGNATURE-----
