Re: [Chimera-users] Saving phi psi values to a text file
Hi Prathvi, In Chimera there is no command to save attributes. Instead you have to use the Render by Attribute dialog's File menu as described in the bottom section of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving> In ChimeraX, as far as I know you can only save one attribute to a file at a time with the "save" command. However, it would probably work just to use the "save" command several times and then (outside of ChimeraX) concatenate the multiple files into one file afterward. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> Another idea is that in ChimeraX you can list attribute values in the Log with the "info" command, e.g. info residues protein attribute phi So an alternative approach if you don't need the file to be in the attribute-file format is to use "info" multiple times and then save the Log contents to an HTML file with "log save" -- see help pages for those commands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> 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 5, 2023, at 10:14 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Is there a command to save the phi and psi angle values of each residue of a PDB file in a text file using UCSF chimera?
I know we can do this in chimeraX using the command: save C:\myphi.defattr attrName phi format defattr model #1
Also, can we use chimeraX to save the phi and psi values in a single file?
Thanks in advance
Very helpful and clear. Thanks one again Elaine! On Sun, Aug 6, 2023 at 10:32 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Prathvi,
In Chimera there is no command to save attributes. Instead you have to use the Render by Attribute dialog's File menu as described in the bottom section of this page: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm...
In ChimeraX, as far as I know you can only save one attribute to a file at a time with the "save" command. However, it would probably work just to use the "save" command several times and then (outside of ChimeraX) concatenate the multiple files into one file afterward. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>
Another idea is that in ChimeraX you can list attribute values in the Log with the "info" command, e.g.
info residues protein attribute phi
So an alternative approach if you don't need the file to be in the attribute-file format is to use "info" multiple times and then save the Log contents to an HTML file with "log save" -- see help pages for those commands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save>
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 5, 2023, at 10:14 AM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Is there a command to save the phi and psi angle values of each residue of a PDB file in a text file using UCSF chimera?
I know we can do this in chimeraX using the command: save C:\myphi.defattr attrName phi format defattr model #1
Also, can we use chimeraX to save the phi and psi values in a single file?
Thanks in advance
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
participants (2)
-
Elaine Meng -
Prathvi Singh