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.
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.
. 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
> -----Original Message-----
> From: pymol-users-admin@...
> [mailto:pymol-users-admin@...] On Behalf Of
> Paul Ha-Yeon Cheong
> Sent: Wednesday, March 23, 2005 3:00 PM
> To: pymol-users@...
> 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,
> PS It is hard to describe the phenomena, so I'm attaching two
> small images to demonstrate what I mean by scrambling versus fine.