To whom it may concern, I would like to know if there's a way to automatically setup a default way for visualising orbitals/densities... that is, after opening a .cube file, to present the density by a specific colour, transparency etc. Thanks a lot! KPZ -- _______________________________________________ Konstantinos P. Zois, MSc PhD student Institute of Theoretical Chemistry, Währinger Str. 17, A-1090 Vienna Department of Chemistry, Universität Wien _______________________________________________
Hello KPZ, I changed the subject line to something more informative. In Chimera, you could define an alias: (1) figure out the Chimera commands that generate the display you want ("volume" etc.) <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> (2) use the "alias" command to define a shorter command that contains all those other ones separated by semicolons ";" see details and examples here <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> (3) your new command would then appear in the Aliases menu if you defined it with "^" (as explained in the link above) (4) later you open an orbital file and then either use the new shorter command in the command line, or choose it from the Aliases menu In ChimeraX, it may be more convenient, since you can define a custom preset with a command file instead of trying to string them all together in a single line: (1) figure out which ChimeraX commands generate the display that you want, and then put them in a command file, see "volume" etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files> (2) use the Preferences, Startup section to define a custom preset from this command file <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> Then you would just open the orbital file and then choose your custom preset from the ChimeraX Presets menu. 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 Jan 17, 2025, at 6:58 AM, Konstantinos P. Zois via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
To whom it may concern,
I would like to know if there's a way to automatically setup a default way for visualising orbitals/densities...
that is, after opening a .cube file, to present the density by a specific colour, transparency etc.
Thanks a lot!
KPZ -- _______________________________________________ Konstantinos P. Zois, MSc PhD student Institute of Theoretical Chemistry, Währinger Str. 17, A-1090 Vienna Department of Chemistry, Universität Wien _______________________________________________
participants (2)
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Elaine Meng -
Konstantinos P. Zois