Hi Sara, I can't think of a fancy way. Probably you need to just select the unwanted atoms and then use Actions... Atoms/Bonds.... delete, or command: delete sel

Usually to avoid this kind of thing from zoning you would use a residue-based cutoff on the zone instead of atoms. Then only whole residues would result.

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 Mar 4, 2024, at 2:40 PM, Sara Luz Gomez Maya via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Hi all, Is there any way to select (or directly remove) atoms without substituents?

The situation is that I have to cut a region of a system. So, after selecting by zone without including the entire residues, I save the selection and I get some single atoms that I would like to get rid of. For example, in the attached file I got H atoms, C atoms, and also C2 chains that do not have any sense even if I complete their valences by adding H. Notice that in such a way they will become H2, CH4 and CH3CH3, respectively, which are very strange molecules for my system that actually contains phospholipids, ibuprofen, and water. I would like to know if there is any automatic tool to do it, for example defining an attribute or using the command line.

Any help is appreciated. Regards, Sara