[Chimera-users] Regarding saving a file

Yash Bahl yashbahl1999 at gmail.com
Sun May 10 11:19:04 PDT 2020

Thank you very much.

On Sun, May 10, 2020, 22:35 Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Yash Bahl,
> Is the question how to get both models in one PDB file?  If you use
> Chimera menu: File... Save PDB, then in the dialog you can choose more than
> oen model to save.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
> However:
> I don't use Pymol or ligplot, so I don't know for sure, but I'm guessing
> they might not use this kind of PDB file with more than one model in it.
> Instead you may need to combine ligand and receptor into one model before
> you save to PDB.
> To combine the ligand and the protein into one model, you can use the
> Model Panel (open from Favorites menu) "copy/combine" function.  You have
> to choose the two models (the ligand and the protein) on the left side of
> the Model Panel and then click "copy/combine" button on the right side of
> the Model Panel.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
> Or, instead of Model Panel, you could use the "combine" command.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
> Then save the new combined model to a PDB file.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On May 10, 2020, at 3:59 AM, Yash Bahl <yashbahl1999 at gmail.com> wrote:
> >
> > Hi,
> > I did a docking experiment from autodock and downloaded the file in
> chimerax format, when I open it works great and I select the model with
> highest delta G and visaulise it, but when I save the model as PDB, and
> open it in pymol only ligand is visible when I open the protein file in the
> same, although the ligand sits perfectly. I am not able to get a PDB file
> of the docked structure for ligplot analysis.
> > Any help would be appreciated.
> > Take care
> > Sincerely,
> >  Yash Bahl
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