Hi Adinda, The form of your command is correct and it doesn't matter which model number is in which place, but you need to add "interSubmodel true" : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html#interSubmodel> #1.1 and #1.2 are submodels of the same model number (#1) and their interactions are ignored unless you use that option. The reason they are ignored by default is that technically in PDB format, submodels of the same model number are supposed to be used for different conformations of the same set of atoms (like NMR ensembles), not different sets of atoms. When people open NMR ensembles they generally don't want to calculate contacts/clashes among the ensemble members. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Dec 27, 2024, at 5:31 AM, ADINDA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimerax team,

Hi, I am trying to find the interactions between my RNA and protein but have been unable to do so. I've been using the "contacts" function but it's not been working as expected. The command line that I gave was: contacts #1.2 restrict #1.1 makePseudobonds true reveal true log true where #1.2 is my RNA and #1.1 is my protein. Even when I switch the positions of #1.2 and #1.1, it still doesn't work (0 contacts shown). Do you have any tips on how I can rectify this? Happy holidays! Best regards, Adinda _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/