Thomas,
The trick for handling these sorts of situations is to load the
first PDB file into PyMOL using "reasonable" atom distances. So long as no
new atoms are added in subsequent PDB files, PyMOL will continue to use the
connectivity from the first state.
The only way to currently change this behavior is to provide the
connectivity you want in the PDB itself using CONECT records and HETATMs
instead of ATOMs.
Why isn't there a reverse play button? Mostly because movies are
generally defined with a series of movie commands that only make sense when
played in a forward sense. If you want to play your movie backwards, you
can easily use the mset command to do this:
For a 100 state movie:
mset 100 -1
mplay
would do the trick.
Or if you want to sweep back and forth:
mset 1 -100 100 -1
or perhaps with pauses at each extreme:
mset 1 x30 1 -100 100 x30 100 -1
Hopefully you get the idea.
Cheers,
Warren
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Thomas Asbury
> Sent: Thursday, April 01, 2004 3:54 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] bond connectivity
>
>
> Hello,
>
> I am making a movie of PDBs files whose atoms get very close
> together and pymol begins to draw all sorts of bond
> connectivity, which is of course correct behavior for
> distance based bonds.
>
> However, these extra bonds seems to stick around even once
> the atoms return to normal positions, that is, the new bonds
> are sorta "sticky". Aren't bonds drawn for each frame
> independently - or is there some context?
> It seems that the first frame is very important.Any way to
> change this behavior ?
>
> I have even tried loading the frames backwards, which does a
> better job since these atoms are further apart in the last frame.
>
> Which brings up another question: why isn't there a reverse
> play button?
> Is there an easy way to play backwards?
>
> Thanks for your help -
> Tom
>
>
>
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