Hi Paul, On Mon, 17 Jan 2011 19:00:09 -0800 Paul Rigor <[email protected]> wrote:
> Hi gang, > Just wondering if anyone has experienced some weird rendering issues, ie, > aberrant bonds between atoms. I've attached a sample pdbqt file which > contains 4 molecules which are outputs of autodock vina. Can someone try > loading and visualizing it? > > I'm currently using the educational version 1.3. I've tried on linux and mac > os x. The nvideo cards include both ATI and NVidia. It isn't really a rendering issue, but a bonding issue (or an atom-ordering issue -- the structures in this multi-model file do not have the same atoms in the same order). You need to load the structures in this multi-model file with the discrete flag turned on. This will force PyMOL to construct a bonding-table for each model separately. load top4fix.pdbqt, discrete=1 Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <[email protected]> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
