Rotation of the multi-model object using the symmetric axis
Dear Chimera-X users! I am dealing with the visualisation of a complex dimer where each monomer is defined as a separate model like #1 and #2. For visualisation purposes I need to rotate the input construct by 180 degrees with the axis of rotation in the middle between the two monomers to avoid the shift of the complex in the x-plane at the end. That's what I have tried: # turn on 180 deg during 10 sec roll y 0.72 250 center #1,2 protein wait 250 but the construct still shifted a bit towards one of the monomers. How could I do ii using the rotation axis, which would be in the center between them ? Many thanks in advance Enrico
You probably have to change the "center" as well. The "axis" is only the direction of rotation. However, I don't know exactly what center will give what you want, you may need to experiment, e.g. with different specifications of x,y,z point in the "center" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/pointspec.html#point> 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 May 31, 2024, at 9:13 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I am dealing with the visualisation of a complex dimer where each monomer is defined as a separate model like #1 and #2. For visualisation purposes I need to rotate the input construct by 180 degrees with the axis of rotation in the middle between the two monomers to avoid the shift of the complex in the x-plane at the end. That's what I have tried:
# turn on 180 deg during 10 sec roll y 0.72 250 center #1,2 protein wait 250
but the construct still shifted a bit towards one of the monomers. How could I do ii using the rotation axis, which would be in the center between them ?
Many thanks in advance
Enrico _______________________________________________ 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/
Hi Enrico, I'd expect your command to rotate about the center of your dimer. But apparently "center #1,2" is not the center of the dimer. Why? I'd guess it is not actually an exact homodimer. You can place a marker (fake atom) at where this center is using marker #3 position #1,2 and then you can try to figure out why that is not the center of the dimer. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html Tom
On May 31, 2024, at 9:13 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I am dealing with the visualisation of a complex dimer where each monomer is defined as a separate model like #1 and #2. For visualisation purposes I need to rotate the input construct by 180 degrees with the axis of rotation in the middle between the two monomers to avoid the shift of the complex in the x-plane at the end. That's what I have tried:
# turn on 180 deg during 10 sec roll y 0.72 250 center #1,2 protein wait 250
but the construct still shifted a bit towards one of the monomers. How could I do ii using the rotation axis, which would be in the center between them ?
Many thanks in advance
Enrico _______________________________________________ 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/
Thank you very much Tom! Would it be useful in this case to determine the centroid of the protein and rotate it along it ? Cheers Enrico Il giorno ven 31 mag 2024 alle ore 21:46 Tom Goddard <goddard@sonic.net> ha scritto:
Hi Enrico,
I'd expect your command to rotate about the center of your dimer. But apparently "center #1,2" is not the center of the dimer. Why? I'd guess it is not actually an exact homodimer. You can place a marker (fake atom) at where this center is using
marker #3 position #1,2
and then you can try to figure out why that is not the center of the dimer.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html
Tom
On May 31, 2024, at 9:13 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I am dealing with the visualisation of a complex dimer where each monomer is defined as a separate model like #1 and #2. For visualisation purposes I need to rotate the input construct by 180 degrees with the axis of rotation in the middle between the two monomers to avoid the shift of the complex in the x-plane at the end. That's what I have tried:
# turn on 180 deg during 10 sec roll y 0.72 250 center #1,2 protein wait 250
but the construct still shifted a bit towards one of the monomers. How could I do ii using the rotation axis, which would be in the center between them ?
Many thanks in advance
Enrico _______________________________________________ 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/
The marker is just to show you where the point is, so that you can use your own visual judgment of whether or not you want to use it as the center of rotation. We don't know which approach will give you the center you want. Elaine
On Jun 3, 2024, at 3:07 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you very much Tom! Would it be useful in this case to determine the centroid of the protein and rotate it along it ? Cheers Enrico
Il giorno ven 31 mag 2024 alle ore 21:46 Tom Goddard <goddard@sonic.net> ha scritto: Hi Enrico,
I'd expect your command to rotate about the center of your dimer. But apparently "center #1,2" is not the center of the dimer. Why? I'd guess it is not actually an exact homodimer. You can place a marker (fake atom) at where this center is using
marker #3 position #1,2
and then you can try to figure out why that is not the center of the dimer.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html
Tom
On May 31, 2024, at 9:13 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I am dealing with the visualisation of a complex dimer where each monomer is defined as a separate model like #1 and #2. For visualisation purposes I need to rotate the input construct by 180 degrees with the axis of rotation in the middle between the two monomers to avoid the shift of the complex in the x-plane at the end. That's what I have tried:
# turn on 180 deg during 10 sec roll y 0.72 250 center #1,2 protein wait 250
but the construct still shifted a bit towards one of the monomers. How could I do ii using the rotation axis, which would be in the center between them ?
Many thanks in advance
Enrico
participants (3)
-
Elaine Meng -
Enrico Martinez -
Tom Goddard