Hi Rino, As far as I know, ChimeraX does not read/show these transition moments directly from ORCA or Gaussian output. There might be something like that in the SEQCROW bundle, but somebody else would have to respond about that. You can create 3D objects arbitrarily using either: (1) a simple file format, BILD. It includes arrows and other shapes. You have to create the file separately in a text editor and then open it in ChimeraX. The format is explained here, with links to example files: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html> (2) the "shape" command, which does not require a separate file. It doesn't have an arrow but you could try making one with cylinder + cone. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.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 Nov 28, 2023, at 5:47 AM, gennaro.pescitelli--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear developers,

first of all, thnak you for your great software, I just started using it. My question: is there a way to plot transition moments (electric and magnetic), as calculated e.g. by TD-DFT calculations in ORCA or Gaussian? If not directly from a log/out file, is tehre a way to manually add a vector arrow?

Thanks

Rino Pescitelli

Hi Rino, It's not the exactly same as in other programs, but there are two approaches: (1) show center of rotation as arrows along XYZ, command: cofr showPivot true ... and you can then use false to turn them off if you want... - OR - (2) use a BILD file, e.g. open the example file "XYZ-axes.bild" linked to the BILD format page: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/XYZ-axes.bild> 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 28, 2023, at 10:39 AM, gennaro.pescitelli--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks so much Elaine,

BILD arrows do what I need. Another (silly?) question: how do I turn on cartesian axes??

Rino

Of course, there is a bild for everything... :) Thanks again Rino

Thank you for the suggestion, I'll see what I can do On Tue, Nov 28, 2023 at 2:02 PM gennaro.pescitelli--- via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Hi Tony,

thank you for you reply. This would be a very useful option in the context of ECD and CPL calculations. I look forward to it.

Another option I may suggest is the possibility to add manual populations or relative energies when averaging a UV or ECD spectrum. The option to select a different file is nice indeed, but sometimes one has populations from a different software or even from experiment (e.g. NMR) or may want to try the effect of different populations on the average spectra.

Thanks a lot

Rino _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/