Matt, Three points:
(1) PyMOL's sculpting feature isn't a forcefield, so it is best to clean up any pose you" sculpt" with a molecular mechanics forcefield minimization afterwards (using external software, such as the Swiss PDB viewer). (2) Unless bonding information is provided in the file, PyMOL connects atoms based on distances. Depending upon your perspective, this is either an annoying limitation or a welcome warning that the structure you've loaded is nonphysical (or at least, far from equilibrium). (3) To save PDB files with explicit bonding and valences using the "multi-CONECT" convention, "set pdb_conect_all" before saving the file. Unfortunately, this feature may be broken or missing in noncurrent builds. Cheers, Warren -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Matt Wagner Sent: Thursday, December 14, 2006 1:03 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Why does the sculpting feature not work? Hi, I constructed a model (.pdb format) and attempted to eliminated some of the excessive contortions in the loop when opened in PYMOL. I was using "Auto-sculpting" to eliminate these contortions. All looked great, but when I saved my work to a .pdb file and opened it back up, it contained broken, stretched, and ugly bonds!!. Perhaps I have am not using the right tool for this task? When I open my model in Swiss PDB Viewer, all is fine. However, I need the graphics and great picture quality that PYMOL creates. Can you tell me a better approach to eliminating contortions in loops in PYMOL or perhaps another program that I should use with just as great graphics? Matt Wagner The Gogonea Group Cleveland, OH 44106 216-875-9723 ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
