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.
<<inline: Ruined.png>>
<<inline: Fine.png>>
_______________________________________
Paul Ha-Yeon Cheong
Member of the K. N. Houk Group
Department of Chemistry and Biochemistry
University of California, Los Angeles
607 Charles E. Young Drive, East
Los Angeles, CA
90095
"A world is supported by four things:
the learning of the wise,
the justice of the great,
the prayers of the righteous
and the valor of the brave."
- Dune, Frank Herbert
