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

[Fernando Luis Cônsoli]

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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