[chimerax-users] How to view swiss docking results in ChimeraX

[Fernando Luis Cônsoli]

Thanks Elaine!

I succeeded in opening the Swiss Dock files in Chimera. And I am just about
to try AutoDock Vina to use the output in ChimeraX even if I have to
convert the .pdbqt file to a .pdb file!

My best,

Fernando

On Thu, Jul 14, 2022 at 3:13 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Fernando,
> Yes, as I said, ChimeraX does not read SwissDock output.
>
> There is a ticket to add this feature, but there has not been any progress
> because we have very many tickets to work on:
> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4232>
>
> My comments about getting the same results for H-bonds, etc. refer to when
> you open files (like PDB files) that both programs can read.
>
> For the ChimeraX tool ViewDockX specifically, here are the docking output
> formats that it can read now:  UCSF DOCK, GOLD, Autodock Vina (.pdbqt),
> Glide Maestro:
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Jul 14, 2022, at 10:47 AM, Fernando Luis Cônsoli via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hi Elaine,
> >
> > Many thanks for your reply. I will try chimera and see if I can make any
> progress. But I am failing to provide the information obtained in Swiss
> Docking to visualize in chimerax the site of interaction predicted in Swiss
> Docking. I did not understand yet how to enter the docking information from
> Swiss Docking in ChimeraX!
> >
> > Many thanks. Fernando
> >
> > On Thu, Jul 14, 2022 at 12:22 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Fernando,
> > Chimera and ChimeraX are two different programs.  Currently, ChimeraX
> does not read the SwissDock clusters output.  However, you can keep using
> Chimera for this purpose (instead of ChimeraX), as shown in the SwissDock
> video.
> >
> > Although there are some differences in the dialogs and command syntax
> between ChimeraX and Chimera, the underlying calculation of clashes,
> contacts, and H-bonds are the same.  So if you use the same values of
> settings, you would get the same results.  So I would say to use whichever
> one you prefer at this time.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Jul 14, 2022, at 5:03 AM, Fernando Luis Cônsoli via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> > >
> > > Hi!
> > >
> > > I am a very excited biologist that has been eagerly trying to use
> ChimeraX to generate hypotheses for the work I collaborate in insect
> resistance to pesticides by analyzing the predicted structure of proteins
> and their interactions with ligands.
> > >
> > > I have been able to generate a 3D model of my protein of interest
> using the alphafold tool as available in ChimeraX. I then proceeded using
> the Swiss Docking tool to predict the interactions of selected ligands with
> the 3D protein model. I can see the results in swiss page, but was not able
> to use the link available to uscf chimera, and neither identify why my
> browser would not launch web chimera when requested.
> > >
> > > I downloaded all the data produced by Swiss Docking, but I can not
> open the clusters.dock4 file generated in my installed version of ChimeraX
> to display the results as it is shown in the video available when selecting
> the link of the uscf chimera in the swiss web page. How can I do that to
> select for the best ligand-protein interaction predicted?
> > >
> > > Alternatively, I have uploaded my protein and ligand pdb files in my
> ChimeraX and calculated clashes and contacts under Structure Analysis in
> the Tools tab, as explained in some of the videos I have been watching with
> the Chimera old version. But I am not confident that what I see reflects
> the prediction data I was able to obtain with the Swiss Docking tool. How
> can I be sure that the ligand-protein interaction predicted this way is the
> best choice?
> > >
> > > Sorry for the long message! Hope someone will bring me some light as I
> struggle with python command lines!
> > >
> > > My best!
> > >
> > > Fernando Consoli
>
>
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