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Hi Greg-- > I've only recently begun using xplor, so I hope this isn't a stupid > question. I am trying to refine the structure of my protein, which > includes a covalently bound acyl phosphopantethein species (about 32 > heavy atoms, and 20 protons. I have a good-looking structure for the > protein, and I want to use xplor to add on the covalently attached > species. I was able to use the addUnknownAtoms method to help out with > this, though I notice that the structure I get out has a large number of > bond, angle, and improper violations. Luckily, this doesn't seem to > matter too much, as subsequent refinement seems to clean up the structure. > a quick call to protocol.fixupCovalentGeom() should also clean things up. Perhaps it should be called as the final step of addUnknownAtoms... > Once the group is attached, I wanted to refine its structure based on > some ambiguous NOE restraints. I've tried using the scripts in > eginput/prot_prot as a model, but I've essentially removed the 'fix' > statements that held portions of the structure rigid. I also found that > the rigid body docking step (rigid_min.inp) wasn't really necessary. (I > had modified this step to allow the attachment to be fully flexible.) > > Couple of questions: > Is there a better script to use as a starting point? What you're doing is probably fine, but why not use one of the Python examples? Is yours a docking problem? > Am I biasing my > results (not sampling enough conformational space) using > sa_cross_tor.inp? that script may be fine. Do note also the ``group'' statements which hold some regions rigid in hpr. cheers-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFDoXsuPK2zrJwS/lYRAl59AJ9fx54rz38jhDrg6WyexCM9UyrabACdE4PT 0YTFX5CEP2A9xkklrclRedg= =64Fx -----END PGP SIGNATURE-----
