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

[Elaine Meng]

Hello,
The main advantage of these plots inside ChimeraX is that they are interactive with the 3D structure (e.g. you click something on the plot, it does something in the 3D window).  They weren't meant for making figures for hundreds of molecules in scripts.   

So, there are no options to customize plot appearance, and the only way to save the histogram currently is by interactively using the context menu on that window, as mentioned in the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>

If you wanted to make your own plots with everything about the appearance customized, currently you would have to write python scripts to dump the data and then use your own favorite plotting program to generate images.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 8, 2022, at 1:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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