Hi Bani, It is impossible to tell what is happening just from that description. I don't know which atoms you have selected or what you want to happen. Did you try command "show atoms" or command "preset sticks" to show all atoms, for example? Remember that if you change the residue to Gly, that glycine residues do not have a side chain. This chimera-users@cgl.ucsf.edu address is for Chimera questions. For the future, if you ask ChimeraX questions please send them to the chimerax-users@cgl.ucsf.edu address instead. If you feel that this is a bug, please save a session, then use menu: Help... Report a Bug and attach the session file that you just saved. Please include a detailed explanation of exactly what you tried and how the result was different from what you wanted to happen, as well as your email address if you would like a response. We need enough details so that we can try exactly the same thing that you tried. 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 30, 2023, at 4:42 PM, Bani Kaur via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. Thank you so much for your help!

Best, Bani Kaur