Good afternoon – I’d appreciate advise for virus capsid viewing. Adeno-associated viruse structures, e.g., 1lp3, consist of the asymmetric unit repeated 60x to form the icosahedral capsid (T=1). I’d like to highlight the equivalent residue in each of the 60 subunits but haven’t figured out how to do that (except by manually going through each of the 60 chains). Please let me know if there are commands that can specify the residue in chains 1, 2, 3,…60. Thank you Robert Kotin
Hi Robert, This is explained in the "atom specification" page -- there are lots of ways to specify atoms, but one way is that ":" means residue name or number, and if you don't specify the chain it will already include that residue number in all chains. Atom specification is the command-line specification of atoms, as could be used in any command that refers to atoms: color, display, repr, etc.: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> Example commands: open biounitID:1lp3 display :314 repr sphere :314 color red,a :314 See help pages for individual commands for their usage (syntax), which will include "atomspec" as detailed in the links above. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> You could also select them, e.g. select :314 ...and then use the Actions menu to act upon them, if you don't want to remember the individual commands, then ~select to deselect them. 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 Aug 13, 2024, at 11:50 AM, Kotin, Robert via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good afternoon – I’d appreciate advise for virus capsid viewing. Adeno-associated viruse structures, e.g., 1lp3, consist of the asymmetric unit repeated 60x to form the icosahedral capsid (T=1). I’d like to highlight the equivalent residue in each of the 60 subunits but haven’t figured out how to do that (except by manually going through each of the 60 chains). Please let me know if there are commands that can specify the residue in chains 1, 2, 3,…60. Thank you Robert Kotin _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Brilliant! Thank you Elaine. rob From: Elaine Meng <meng@cgl.ucsf.edu> Date: Tuesday, August 13, 2024 at 3:39 PM To: Kotin, Robert <Robert.Kotin@umassmed.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>, Robert Kotin <kotinr@mit.edu> Subject: specifying residues in Chimera Hi Robert, This is explained in the "atom specification" page -- there are lots of ways to specify atoms, but one way is that ":" means residue name or number, and if you don't specify the chain it will already include that residue number in all chains. Atom specification is the command-line specification of atoms, as could be used in any command that refers to atoms: color, display, repr, etc.: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fframeatom_spec.html&data=05%7C02%7CRobert.Kotin%40umassmed.edu%7C800b2f654ee74ae0713e08dcbbcfa374%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C638591747710018315%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=tRdMp0umLHbRkMIIli1N2PAmrsJGgvRIEFK%2BmZ9htu8%3D&reserved=0<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fatom_spec.html%23basic&data=05%7C02%7CRobert.Kotin%40umassmed.edu%7C800b2f654ee74ae0713e08dcbbcfa374%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C638591747710029881%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=RXHlOMihnLh4VZlDB3pkl%2B1ZdxljSiaDTDen8fhvgjQ%3D&reserved=0<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic>> Example commands: open biounitID:1lp3 display :314 repr sphere :314 color red,a :314 See help pages for individual commands for their usage (syntax), which will include "atomspec" as detailed in the links above. <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fframecommand.html&data=05%7C02%7CRobert.Kotin%40umassmed.edu%7C800b2f654ee74ae0713e08dcbbcfa374%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C638591747710036497%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=bMryR%2FqlLjefUM45ws5VFe6HBsZ%2Fv6FQK0atS1wA4BQ%3D&reserved=0<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>> You could also select them, e.g. select :314 ...and then use the Actions menu to act upon them, if you don't want to remember the individual commands, then ~select to deselect them. 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 Aug 13, 2024, at 11:50 AM, Kotin, Robert via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good afternoon – I’d appreciate advise for virus capsid viewing. Adeno-associated viruse structures, e.g., 1lp3, consist of the asymmetric unit repeated 60x to form the icosahedral capsid (T=1). I’d like to highlight the equivalent residue in each of the 60 subunits but haven’t figured out how to do that (except by manually going through each of the 60 chains). Please let me know if there are commands that can specify the residue in chains 1, 2, 3,…60. Thank you Robert Kotin _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimera-users%40cgl.ucsf.edu%2F&data=05%7C02%7CRobert.Kotin%40umassmed.edu%7C800b2f654ee74ae0713e08dcbbcfa374%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C638591747710040996%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=VKE%2FvEVb%2F0JSkjGQGPozIqTHIzdmQdzTBEP%2FcDL62Sw%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/>
participants (2)
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Elaine Meng -
Kotin, Robert