transition dipole moments
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, 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
Thanks so much Elaine,
BILD arrows do what I need. Another (silly?) question: how do I turn on cartesian axes??
Rino
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
Rino,
seqcrow currently does not have a way to show the transition vectors. I'll look into adding a command for that in the next version.
Best,
Tony
On Tue, Nov 28, 2023 at 12:12 PM Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
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
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/
Of course, there is a bild for everything... :)
Thanks again
Rino
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
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/
participants (3)
-
Elaine Meng
-
gennaro.pescitelli@unipi.it
-
Tony Schaefer