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, <[email protected]> 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----- >
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