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

[Elaine Meng]

Hi Fernando,
You do not have to convert Autodock Vina output.  The ChimeraX ViewDockX tool should already understand the pdbqt file from Autodock Vina.
<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 15, 2022, at 5:39 AM, Fernando Luis Cônsoli via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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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