[Chimera-users] Regarding saving a file

[Ammar Jastaniah]

Thank you for your help Elaine.

Ammar

On Mon, May 11, 2020 at 10:55 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ammar,
> Typically you can use one of many docking programs separately from
> Chimera: UCSF DOCK, Glide, GOLD, AutoDock, AutoDock Vina, SwissDock, etc.
> You just have to download that other program (or use a web service) to do
> the docking, instead of using Chimera.
>
> Then, after you get the output file you can use Chimera's ViewDock tool to
> view and analyze the results.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html
> >
>
> For example, see the Swissdock website, which includes a video of using
> Chimera to view the results:
> <http://www.swissdock.ch/>
>
> 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 2:36 PM, Ammar Jastaniah <ajasta2 at uic.edu> wrote:
> >
> > Hi,
> >
> > 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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