[Chimera-users] Regarding saving a file

Ammar Jastaniah ajasta2 at uic.edu
Sun May 10 14:36:39 PDT 2020


But I thought that the Autodock Vina function has been discontinued since
April 30th as I have been having trouble docking my compound. Is there any
way around this?

Thank you

Ammar Jastaniah

On Sun, May 10, 2020 at 1:22 PM Yash Bahl <yashbahl1999 at gmail.com> wrote:

> 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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