Dear community, Is there a way to show only the Ca backbone trace? Looks like this was a while ago in the forum (https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...) so was wondering if it is now possible to do so in ChimeraX. Thanks, Abhi
Wow, that's an old message! I'd forgotten there was ever a time where you could not show it. Yes, for chain trace you would just hide the protein ribbon and hide protein atoms except CA, for example: open 4hhb hide ribbons hide protein show @ca In that example, you can then use the disclosure triangle in the Models panel to see that there is a model #1.2 named chain trace. The lines between the CA atoms are pseudobonds, and you can change their thickness in various ways, such as with the Selection Inspector GUI (after selecting one or more of the pseudobonds), or the size command: size #1.2 pseudobondrad .15 See: <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html> 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 26, 2025, at 9:33 AM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear community, Is there a way to show only the Ca backbone trace? Looks like this was a while ago in the forum (https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...) so was wondering if it is now possible to do so in ChimeraX. Thanks, Abhi
Hi Elaine, This is very helpful. Thanks a lot! Abhi From: Elaine Meng <meng@cgl.ucsf.edu> Date: Thursday, June 26, 2025 at 1:10 PM To: Das, Abhinaba <abhinaba.das@emory.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [External] Re: [chimerax-users] Ca-trace [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Wow, that's an old message! I'd forgotten there was ever a time where you could not show it. Yes, for chain trace you would just hide the protein ribbon and hide protein atoms except CA, for example: open 4hhb hide ribbons hide protein show @ca In that example, you can then use the disclosure triangle in the Models panel to see that there is a model #1.2 named chain trace. The lines between the CA atoms are pseudobonds, and you can change their thickness in various ways, such as with the Selection Inspector GUI (after selecting one or more of the pseudobonds), or the size command: size #1.2 pseudobondrad .15 See: <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fpseudobonds.html&data=05%7C02%7Cabhinaba.das%40emory.edu%7Cb95a4eeeaeb14444fe6c08ddb4d45902%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638865546325038670%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2Bt6xO28bncVKk%2FyzZmgk1DXv8AWzpqVUZf%2By7Wc4WTI%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>> <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Finspector.html&data=05%7C02%7Cabhinaba.das%40emory.edu%7Cb95a4eeeaeb14444fe6c08ddb4d45902%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638865546325062105%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=yySCZM%2FLSYrEB6Thad5vrgruBmW2J7QmyIqXbik%2FvsE%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html>> <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fsize.html&data=05%7C02%7Cabhinaba.das%40emory.edu%7Cb95a4eeeaeb14444fe6c08ddb4d45902%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638865546325079022%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=lFkF03kTIl8tfB1kXpXrbQi43piJomhDidZ7bES5KyI%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html>> 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 26, 2025, at 9:33 AM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear community, Is there a way to show only the Ca backbone trace? Looks like this was a while ago in the forum (https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2Fthread%2FFMHUBATANG46EVVTHLNLN5EKCNH65R53%2F%23FMHUBATANG46EVVTHLNLN5EKCNH65R53&data=05%7C02%7Cabhinaba.das%40emory.edu%7Cb95a4eeeaeb14444fe6c08ddb4d45902%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638865546325094985%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=x1OoVRxHhL494SN%2FbiH7rpWk1NS3ciHP4pC6nGWrTmo%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/FMHUBATANG46EVVTHLNLN5EKCNH65R53/#FMHUBATANG46EVVTHLNLN5EKCNH65R53>) so was wondering if it is now possible to do so in ChimeraX. Thanks, Abhi
participants (2)
-
Das, Abhinaba -
Elaine Meng