[chimerax-users] 2D plots and graphs for protein-ligand interactions

[Elaine Meng]

Hello!
The chain contacts diagram shown in Fig 4b is made with the "interfaces" command.  Then you can use context menu on that contacts diagram to make the interface-residue plot in Fig 4d.  Please see the "interfaces" help for details on both of those.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>

The histogram plot in Fig 5b  is made with the command "crosslinks histogram" but first you have to have some crosslinks, or other pseudobonds such as from finding H-bonds or contacts.  Then in the "crosslinks histogram" command you specify the pseudobond model to plot their distances.  See "crosslinks histogram" help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>

Also for a more detailed example see the "Interactive H-bond Histogram" feature highlight, which includes a script (.cxc file):
<https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 7, 2022, at 2:18 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX users!
> I am dealing with the analysis of protein-ligand interactions in a
> single PDB structure. I am looking for any tools implemented in
> Chimera-X, which could be used to analyse the interactions (besides
> the hbond and contact tools giving info in the log files).
> I wonder to know which commands and corresponded ChimeraX tools could
> be used to produce the 2D contact diagrams shown on the Fig.4 as well
> as python graphs demonstrated on the Fig.5 in the Chimera-X article:
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/
> 
> Many thanks in advance!
> Cheers
> Enrico