Saving omega angles to file
Hello Elaine, Is there a way to save the omega angle of residues to a file using either chimera or chimeraX? I am able to save the phi, psi, chi angles using the *Render by attribute *tool in chimera but I could not find a way to save the omega angle. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
In Chimera it’s not possible with writing a Python script. In ChimeraX it’s: save <folder to save in>/omega.defattr attr omega --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 16, 2022, at 9:07 PM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello Elaine,
Is there a way to save the omega angle of residues to a file using either chimera or chimeraX? I am able to save the phi, psi, chi angles using the Render by attribute tool in chimera but I could not find a way to save the omega angle.
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
…without writing a Python script...
On Nov 17, 2022, at 10:01 AM, Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
In Chimera it’s not possible with writing a Python script. In ChimeraX it’s:
save <folder to save in>/omega.defattr attr omega
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 16, 2022, at 9:07 PM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Hello Elaine,
Is there a way to save the omega angle of residues to a file using either chimera or chimeraX? I am able to save the phi, psi, chi angles using the Render by attribute tool in chimera but I could not find a way to save the omega angle.
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Thanks once again Eric. I have two more questions. Is the "Render by Attribute" tool available in chimeraX because I get nothing when I run the command: *ui tool show "Render by Attribute". *If it isn't available, can I expect it to be added to chimeraX in the future? Is there a command to save attributes of a residue in chimera (not chimeraX; that you covered in the previous reply) On Thu, Nov 17, 2022 at 11:33 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
…with*out* writing a Python script...
On Nov 17, 2022, at 10:01 AM, Eric Pettersen via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
In Chimera it’s not possible with writing a Python script. In ChimeraX it’s:
save <folder to save in>/omega.defattr attr omega
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 16, 2022, at 9:07 PM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hello Elaine,
Is there a way to save the omega angle of residues to a file using either chimera or chimeraX? I am able to save the phi, psi, chi angles using the *Render by attribute *tool in chimera but I could not find a way to save the omega angle.
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Prathvi, There is a different address for ChimeraX questions, chimerax-users@cgl.ucsf.edu CC'd here. You can see the currently available tools listed in the ChimeraX User Guide, and links to their pages: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> ... and the dates that they were added in the ChimeraX Change Log <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> ... so yes, we just started adding Render by Attribute to ChimeraX, but you have to get a recent daily build of version 1.6, and it does not have many options yet. Only ChimeraX (not Chimera) has a command to save attributes to a file. In Chimera you have to use the GUI. In ChimeraX we are specifically trying to make commands for all or nearly all actions you can perform with the GUI. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 18, 2022, at 4:23 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thanks once again Eric. I have two more questions. Is the "Render by Attribute" tool available in chimeraX because I get nothing when I run the command: ui tool show "Render by Attribute". If it isn't available, can I expect it to be added to chimeraX in the future? Is there a command to save attributes of a residue in chimera (not chimeraX; that you covered in the previous reply)
participants (3)
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Elaine Meng -
Eric Pettersen -
Prathvi Singh