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

[Elaine Meng]

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