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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