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Hi Greg-- > > > > a quick call to protocol.fixupCovalentGeom() should also clean things > > up. Perhaps it should be called as the final step of addUnknownAtoms... > Thanks very much. > That does work quite well. However, there is a slight problem with > fixupCovalentGeom() as it stands. If you only run it on a portion of a > covalent structure, it will violate restraints between the selected and > unselected part of the molecule. I've attached the fix as a patch - > it changes the constraint definition to allow constraints between the > selected and unselected parts of a molecule. > thanks so much for the patch. I've been meaning to fix that. > The only problem with sticking fixupCovalentgeom into addUnknownAtoms is > that you would probably have to export the fixupCovalentgeom parameters to > the function call for addUnknownAtoms - I had to change maxIters to get > fixupCovalentgeom to get the structure right. I'll hold off on this step for now- I would like to merge the functionality of these two routines anyway, since addUnknownAtoms does fixupCovalentGeom... It also may be worthwhile > to mention in the documentation that fixupCovalentgeom changes the > 'constraints' setting, depending on what the user wants to do afterwards. agreed. > > > > > > 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? > The main reason was because I have had a little bit more exposure to the > xplor interface and am not as sure of things with the python interface. > > My problem isn't truly a docking problem, but I'm treating it similarly to > a docking problem. ...but it is a docking problem. I understand. It sounds like you're on the right track. Please let me know if you have any other questions. regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFDoz07PK2zrJwS/lYRAlYlAJwKCaqC9O0qxq+llBO0efcXm8Du1QCfdyx6 w7TPgUqTIfU4skLH1w5HmXY= =1tg4 -----END PGP SIGNATURE-----
