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 <rsengupta@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 <rsengupta@wisc.edu')" target="1">rsengupta@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&#39;m using spheres instead, but wondering if there&#39;s a way to work around the problem and still view the ligands as sticks/lines.
> >
> >
> > Thanks,
> > Ritu
> >
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