Dmitry, VMD may have the ability to shift and recombine the molecule relative to the periodic boundary in order to avoid this dismembered effect, whereas currently PyMOL does not. I believe ptraj can do this for you, though it has been ages since I have tried using PyMOL with Amber.
Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Dmitry Kondrashov > Sent: Saturday, November 19, 2005 9:57 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] problem with amber trajectory > > Hi, > > I have a prloblem with viewing AMBER trajectory files, > specifically, the topology appears messed up. When I load the > trajectory into the topology object, the structure shows up > dismembered into eight pieces on the vertices of a cude. I > should note that I can load an AMBER coordinate file into the > same topology with no problem, and that the trajectory > displays just fine in VMD. > I'm using MacPyMol on Mac OS 10.4.3. No error messages appear > in loading the trajectory, here's the last few lines: > > ObjectMolecule: read set 757 into state 757... > ObjectMolecule: read set 758 into state 758... > CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w". > CmdLoadTraj: 758 total states in the object. > > I appreciate your help, > Dmitry > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get > Certified Today Register for a JBoss Training Course. Free > Certification Exam for All Training Attendees Through End of > 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
