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

[Enrico Martinez]

Thanks a lot, Elaine!
Actually crosslink hist #1 works very well!
Could you please specify would it be possible to plot the histogram
(using batch chimera-x execution) or alternatively add it directly to
the produced png image?
I did not find any possibility to save the plot or to customize its
appearance (color of the bars etc).
Cheers
Enrico

Il giorno mer 7 set 2022 alle ore 17:52 Elaine Meng
<meng at cgl.ucsf.edu> ha scritto:
>
> 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
>