Dear All, I am trying to build a single PDB file from two different PDB files. One PDB has a small organic ligand, and the second PDB contains amino acid side chains from an active site.
I load both PDB files, but I want to "freeze" the orientation of the amino acid side chains PDB ( not move it), and then place and orient the ligand PDB in a certain pose with respect to the amino acid side chains. Ideally, I would then like to save the coordinates for both the amino side chains and the ligand coordinates to a single PDB file. In the long run, I want to run a simple minimization on an possible active site cluster and I want to get a feel for the energetics of the ligand in the active site. I don't like working with MOLDEN or some of the other suites out there and I wanted to try this with PyMOL. I've gone through the manual, the web, pymolwiki, the "masking" and "protecting" options, and I've tried examining the use of frames and split_states, but I haven't come up with anything. I've heard about a demo that Warren DeLano put on for the ACS where, as part of the demo, he showed off some toy example where he docked a ligand in by hand, complete with having PyMOL show red/green dots for steric clashes/matches. Any ideas? -Mark ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
