Hi Elaine, I want to select all the atoms except the backbone oxygen and nitrogen atom of residues 100.A to 120.A . Is there a command to do this in either chimera or chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Prathvi, (1) Yes, both programs easily allow specifying something and not something. Please see the help pages so you can learn for yourself how to generalize to other situations. In these examples & means intersection (and) and ~ means negation (not). ChimeraX command sel /A:100-120 &~ @C,N ChimeraX command-line specification help page <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Chimera command sel :100-120.A &~ @C,N Chimera command-line specification help page <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> (2) Alternatively, in either program you could do it in two steps, i.e., one command for selecting all the atoms in that residue range and then in a second command, deselecting specific atoms by name. (3) Did you really want to select the backbone O? If not, then it would be C,N,O in these commands instead of just C,N I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2023, at 12:28 AM, Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I want to select all the atoms except the backbone oxygen and nitrogen atom of residues 100.A to 120.A . Is there a command to do this in either chimera or chimeraX?
Yes I wanted to exclude the backbone O and N-atoms from my selection. I applied your method and it is working perfectly. Thank you so much! On Fri, Aug 4, 2023 at 9:44 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Prathvi, (1) Yes, both programs easily allow specifying something and not something. Please see the help pages so you can learn for yourself how to generalize to other situations. In these examples & means intersection (and) and ~ means negation (not).
ChimeraX command
sel /A:100-120 &~ @C,N
ChimeraX command-line specification help page <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
Chimera command
sel :100-120.A &~ @C,N
Chimera command-line specification help page < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
(2) Alternatively, in either program you could do it in two steps, i.e., one command for selecting all the atoms in that residue range and then in a second command, deselecting specific atoms by name.
(3) Did you really want to select the backbone O? If not, then it would be C,N,O in these commands instead of just C,N
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2023, at 12:28 AM, Prathvi Singh via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I want to select all the atoms except the backbone oxygen and nitrogen atom of residues 100.A to 120.A . Is there a command to do this in either chimera or chimeraX?
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
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Prathvi Singh