Thanks, Charles. It looks work well. If I want to apply more sets of
position restraints, I just need to setup refRMSD3, refRMSD4, etc. like
that, isn't it?
Thanks,
Xiaogang
On Wed, Aug 5, 2009 at 10:39 AM, <Charles at schwieters.org> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
>
> Hello Xiaogang--
>
> >
> > I am trying to refine a crystall structure with one set of RDCs. In
> > this refinement, I need to apply position restraints to keep the whole
> > protein folded correctly. What I do was keep the the backbone atoms of
> the
> > residues which have secondary structures in the postion of the original
> > structure. The position restraints are applied as below:
> > "
> > from posDiffPotTools import create_PosDiffPot
> > refRMSD = create_PosDiffPot("refRMSD",
> > "(resid 2:7 or resid 10:16 or resid 23:34 or
> > resid 38:44 or resid 56:59 or resid 66:71) and (name CA or name N or name
> C)
> > ",
> > pdbFile="ubnmr.pdb")
> > refRMSD.setUpperBound(0)
> >
> > refRMSD.setScale(10000)
> >
> > potList.append(refRMSD)
> > "
> > After the refinement, most secondary structure folded correctly. But
> > several B strands do not folded well. I want to applied higher energy
> just on
> > these residues which do not folded well. Thus I need to setup two set of
> > position restraints like above, but with different energy. I do not know
> how
> > to do that. Does anyone know how to do that?
> >
>
> how about:
>
> refRMSD2 = create_PosDiffPot("refRMSD2",
> """other selection""",
> pdbFile="ubnmr.pdb")
> refRMSD2.setUpperBound(0)
> refRMSD2.setScale(1e6)
> potList.append(refRMSD2)
>
>
> best regards--
> Charles
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.9 (GNU/Linux)
> Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/>
>
> iEYEARECAAYFAkp5maAACgkQPK2zrJwS/laBOwCfQU7LyC+Z4OWKVh5lAPWyLq4D
> y0wAn2sQKh8ZVsMGKpbAKae55y8qeg08
> =HZJJ
> -----END PGP SIGNATURE-----
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20090805/29c2d3e5/attachment.html
