Hi Dmitry, DIMPLOT (for drawing 2D diagrams of interactions) is not in Chimera or ChimeraX, sorry. People usually use Ligplot or Discovery Studio Visualizer to do something like that. As for finding contacts: simple, yet not that simple, because there are many ways to do it. You could always do a simple zone selection (atoms within some distance of some other atoms), menu: Select... Zone <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#selectzone> command-line zone specification <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones> ...but there are several tools and commands specifically for finding contacts: menu: Select... Contacts, with several options <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> Contact-related tools include: Contacts Clashes (both are similar to Chimera's Find Contacts/Clashes) <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> Contact-related commands include: contacts clashes <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> interfaces <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html> The help pages linked above explain all othe options, but there are also examples in tutorials, for example "Protein-Ligand Binding Sites" includes finding H-bonds and contacts: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 6, 2023, at 3:04 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Probably very simple question, non the less - how to calculate&show the contacts/clashes in the model?
We have heptamer and we would like to find out what are the contacts & clashes with 6 surrounding units.
I know that chimera can do that.
Also, I heard that there is also software called DIMPLOT. Does ChimeraX do the same?
Thank you in advance.
Sincerely, Dmitry