Dear developers, I have a question I'd like to ask. The structure after refinement appears as helices when opened in PyMOL, but in ChimeraX, it doesn't display as helices, as shown in the figures. What could be the reason for this? Is there a way to make it display as helices in ChimeraX? Looking forward to your answer, thank you！ Best regards, Nan 张楠 zhangnan@nankai.edu.cn
Dear Nan, Different programs use slightly different rules to automatically detect "helix" and "strand" in structures when the files do not already include these assignments. So probably ChimeraX default assignment did not assign that part as helix. However, you can assign it manually, for example, if that part is already selected like in your ChimeraX image, (1) choose menu: Actions... Inspect (2) in the resulting Selection Inspector, Inspect "Residues" and then change the Secondary structure type to "helix" Selection Inspector help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html> Or, you could do it with a command: setattr sel r ss_type 1 "setattr" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html> names and values of residue attributes (ss_type: 0 for coil, 1 for helix, 2 for strand): <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> If you didn't have the residues selected, you could specify them directly in the command, for example, residues 61-69 in chain A: setattr /A:61-69 r ss_type 1 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 6:09 AM, 张楠 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear developers, I have a question I'd like to ask. The structure after refinement appears as helices when opened in PyMOL, but in ChimeraX, it doesn't display as helices, as shown in the figures. What could be the reason for this? Is there a way to make it display as helices in ChimeraX?
Looking forward to your answer, thank you！ Best regards, Nan
张楠 zhangnan@nankai.edu.cn
Dear Elaine, Thank you very much for your response! Both methods are very effective and resolved my issue. I sincerely appreciate your help. Best regards, Nan 张楠 zhangnan@nankai.edu.cn ---- Replied Message ---- From Elaine Meng via ChimeraX-users<chimerax-users@cgl.ucsf.edu> Date 3/5/2024 08:26 To 张楠<zhangnan@nankai.edu.cn> Cc "chimerax-users@cgl.ucsf…"<chimerax-users@cgl.ucsf.edu> Subject [chimerax-users] how to show ribbon as helix not coil Dear Nan, Different programs use slightly different rules to automatically detect "helix" and "strand" in structures when the files do not already include these assignments. So probably ChimeraX default assignment did not assign that part as helix. However, you can assign it manually, for example, if that part is already selected like in your ChimeraX image, (1) choose menu: Actions... Inspect (2) in the resulting Selection Inspector, Inspect "Residues" and then change the Secondary structure type to "helix" Selection Inspector help: <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_docs_user_tools_inspector.html&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=cL0WvLW074DHXNhkYyxmeHhSv30WxTDLNOf7i2e1T40&m=pI7c0uo0ZCXHyzDPWvIUoep2eO684Igu4IaRUGdYPv06vkazpNi7Fp-miMWeF9vF&s=Pgor2dIzFaqexWnbn-fElvqb3l4YJiRHCFwi0COsWrg&e=> Or, you could do it with a command: setattr sel r ss_type 1 "setattr" help: <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_docs_user_commands_setattr.html&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=cL0WvLW074DHXNhkYyxmeHhSv30WxTDLNOf7i2e1T40&m=pI7c0uo0ZCXHyzDPWvIUoep2eO684Igu4IaRUGdYPv06vkazpNi7Fp-miMWeF9vF&s=f4F8e1Zu0tABowGMc6oaQBjg0PSVg8y2bxsM4ETxBcE&e=> names and values of residue attributes (ss_type: 0 for coil, 1 for helix, 2 for strand): <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_docs_user_attributes.html-23residue&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=cL0WvLW074DHXNhkYyxmeHhSv30WxTDLNOf7i2e1T40&m=pI7c0uo0ZCXHyzDPWvIUoep2eO684Igu4IaRUGdYPv06vkazpNi7Fp-miMWeF9vF&s=xGJ1aYm3HkbM5ztwirU9I8S7_-0QD5yTIXuLCAfeNJw&e=> If you didn't have the residues selected, you could specify them directly in the command, for example, residues 61-69 in chain A: setattr /A:61-69 r ss_type 1 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 6:09 AM, 张楠 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear developers, I have a question I'd like to ask. The structure after refinement appears as helices when opened in PyMOL, but in ChimeraX, it doesn't display as helices, as shown in the figures. What could be the reason for this? Is there a way to make it display as helices in ChimeraX? Looking forward to your answer, thank you！ Best regards, Nan 张楠 zhangnan@nankai.edu.cn _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.cgl.ucsf.edu_mailman_archives_list_chimerax-2Dusers-40cgl.ucsf.edu_&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=cL0WvLW074DHXNhkYyxmeHhSv30WxTDLNOf7i2e1T40&m=pI7c0uo0ZCXHyzDPWvIUoep2eO684Igu4IaRUGdYPv06vkazpNi7Fp-miMWeF9vF&s=wQhdJSi2oO_xXHAeZ0EQphf_GmUjSc-FAvas5UOBuwE&e=
participants (2)
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Elaine Meng -
张楠