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

[Fernando Luis Cônsoli]

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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