Jack, What are all those extra "Q" atoms in the pdb file? They look to me like compromise/placeholder coordinates for NMR-equivalent hydrogens...or something like that.
To get a reasonable picture, you can get rid of the extra bonds with unbond elem q*,all or just nuke the "Q" atoms altogether remove q* Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -----Original Message----- > From: Jack Howarth [mailto:howa...@bromo.msbb.uc.edu] > Sent: Sunday, January 12, 2003 6:17 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] 1pit.pdb > > > Under linux does anyone else see the following? If one > loads in the 1pit.pdb from the MOLMOL data files, the > resulting structure seems to have extra bonds drawn in the > side chains. For example phe's seem to have all the opposing > carbons in the rings interconnected through the center of > the ring. Thanks in advance for any hints on what is causing > that. > Jack > > > ------------------------------------------------------- > This SF.NET email is sponsored by: > SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! > http://www.vasoftware.com > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
