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@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@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