how to select atoms without substituents?

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

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
participants (2)
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Elaine Meng
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Sara Luz Gomez Maya