Hi kmeatball,
If you append all structures to the same model, which is what you do
by loading each under the same name into different states, the
connectivity will be determined by the first state. That is, the
"topology information" (read bond map) is global, and applies to all
states. If you want to have the connectivity change during the movie,
you have to load each file separately. You could first make a script
which determines the appearance and the view (get_view/set_view) and
do something like:
for file in filelist:
cmd.load(file,"mov")
cmd.do("@settings.pml")
cmd.ray()
cmd.png(file[:-3]+"png")
cmd.delete("mov")
Hope it helps,
Tsjerk
On 9/10/07, Killer Meatball <kmeatb...@excite.com> wrote:
>
> Hi,
>
>
>
> I'm loading a sequence of .pdb files into a movie using the script:
>
>
>
> for file in file_list:
>
> cmd.load(file,"mov")
>
>
>
> cmd.mset("1 -%d"%len(file_list))
>
>
>
> The problem is that some bonds (conect records in the .pdb files)
>
> are persisting in the movie even after they are no longer in the
>
> .pdb.
>
>
>
> Is there a way to get pymol to refresh the bonds in every frame
>
> of the movie?
>
>
>
> Thanks in advance,
>
> kmeatball
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
