Paul, Set the "discrete=1" option to the load command when loading multiple small molecules from a PDB. Otherwise, PyMOL will attempt to match them up atom for atom based on name, applying connectivity from the first state.
Cheers, Warren PS. Humorous aside: Wow: "factory settings" -- I like that. The ol' "garage settings" just didn't quite have the same ring to it. We don't just have an office now, we have a software factory -- fantastic! -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . 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 > Paul Ha-Yeon Cheong > Sent: Wednesday, March 23, 2005 3:00 PM > To: pymol-users@lists.sourceforge.net > Cc: Paul Ha-Yeon Cheong > Subject: [PyMOL] How do you reset to default > bonds/connectivity for all states in an object? > > Dear Pymol users, > > I am trying to use Pymol to make PNG frames in order to merge > them into a movie. I am interested in small molecule > vibrational animation. > > I have a series of PDB files containing the coordinates for > the molecular motion for each of the frames of the movie. I > am using a '*.pml' script to load each of the individual pdb > files as states in an object. > > Everything is fine, except that after the first two states, > the bonds for the other states all scramble. In the first > state or two, the default bonding detection by pymol does a > great job at reproducing exactly what I want, but after > these, all the bonds between atoms are completely scrambled. > If I load the pdbs individually, they all appear fine, with > the desired bonds/connectivity. > > Is there a way to reinstate the default bonds/connectivity > detection for all states in an object? I have tried 'dss' and > 'rebuild' commands, but they do not seem to help. I am using > the factory settings of MacPymol on a G5. > > Please let me know if there is a way to fix this problem or > if I should provide more details to describe my problem. > > Best regards, > Paul. > > > PS It is hard to describe the phenomena, so I'm attaching two > small images to demonstrate what I mean by scrambling versus fine. > > >
