Hi Tim, Long answer to a short question, I'm afraid... There are several different ways you can find interactions: (A) simple distance zones from some set of atoms, or (B) chain-chain contacts based on surface area, or (C) atom-atom contacts based on distance but corrected for different VDW radii of different atom types, or (D) atom-atom H-bonding interactions specifically. You can also color protein surfaces by their electrostatic potential or lipophilic potential to get an idea of the properties of their binding regions. Approach (A): select other atoms within a simple distance zone of specified atoms (1) select the atoms of interest, could be all RNA (e.g.: command "select nucleic" assuming there's no DNA) or one specific RNA chain at a time as you prefer (e.g. menu: Select... Chain... [specific chain ID]) (2) menu: Select... Zone <https://www.rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> Approach (B): chain-chain interfaces based on buried surface area. This may not be what you want, given that you want to include water and ions, not just biopolymer chains. If you did want it, however, you could take a look at the "interfaces" command and/or (1) select RNA as in (A) (2) menu: Select... Contacts, choose the "Chains" option <https://www.rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html> Approach (C): atom-atom contacts based on distance and VDW radii. Use the "contacts" command, menu: Tools... Structure Analysis... Contacts, and/or (1) select RNA as in (A) (2) menu: Select... Contacts, choose the "Atomic" option <https://www.rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> Approach (D): H-bonds. Use the "hbonds" command and/or menu: Tools... Structure Analysis... H-Bonds <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> There are examples of H-Bonds, Contacts (atomic), and coloring protein surfaces by ESP and MLP in the binding sites tutorial: <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 Nov 6, 2023, at 10:30 AM, tim smith via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
How do we select a zone in ribosomal RNA (nucleotide residues of rRNA) to visualize all its interaction interfaces with ribosomal proteins/H2O/ions using ChimeraX? Thank you for your support. Thank you. Best Tim