Ritu,
just an idea. It could be that your PDB files contains CONECT records
for your ligands. Those bonds are defined by atom number or atom index I
believe. There could be a conflict between the different files you are
loading. Try stripping the CONECT records and see if that helps.
HTH
Carsten
From: Folmer Fredslund [mailto:folm...@gmail.com]
Sent: Wednesday, May 23, 2012 1:53 PM
To: Rituparna Sengupta
Cc: PyMol Users Mailing List
Subject: Re: [PyMOL] Messed up structures in movie
Hi again Ritu,
This does seem odd. I have no idea what might be wrong, but could you
provide an example pdb, or a png of the output you see?
I would personally try to strip all extra information from the ligand
pdb (so only ATOM and HETATM records is included) and then try loading
that pdb.
Best regards,
Folmer
2012/5/23 Rituparna Sengupta <rsengu...@wisc.edu>
Hi,
Sorry about the lack of description in the previous post.
The chemicals show incorrect bond connections. Some of the rings go
missing. In all, the structure changes and just by looking at it, its
possible to tell that the structure is not right. I didn't see much
details though, except that the atom connections seem to be wrong.
Thanks,
Ritu
On 05/23/12, Folmer Fredslund
wrote:
> Hi Ritu,
>
> Could you elaborate on "some of the ligand structures get completely
messed up when viewed as sticks or lines"?
>
> To get the best possible answer a few more details would help.
>
> Best regards,
> Folmer
>
> 2012/5/23 Rituparna Sengupta <PyMOL-users@lists.sourceforge.net
<rsengu...@wisc.edu')" target="1">rsengu...@wisc.edu>
>
> > Hi,
> >
> > Just observed something weird. When I try loading protein -ligand
complexes as frames of a movie (same protein but different ligands for
different frames), some of the ligand structures get completely messed
up when viewed as sticks or lines. Right now I'm using spheres
instead, but wondering if there's a way to work around the problem
and still view the ligands as sticks/lines.
> >
> >
> > Thanks,
> > Ritu
> >
> >
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