Dear Chimera team, I hope you are well.
I am processing a phage dataset which presents D5 pseudossymetry. The C5 axys is aligned to the z axys. I would like to rotate the map 90 degree in the z axys, so that Z axys now separate the molecule in a C2 pseudosymmetry, in order to play with some symmetry relaxation features to refine differences in the two map vortexes. Is there a way in chimera to rotate the map in relation to the xyz axys? The way I see, all rotate commands I know rotate the axys themselves alongside the map.
Thank you for your time, Kind wishes, Leonardo
Hi Leonardo, If I understand correctly, I think you can use the "models" option (e.g. "model #2") of the "turn" command or other movement commands like "roll" and "move" to move only the specific model instead of the whole scene. The axis specification in the command also allows you to control the orientation of the rotation: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html
However, if it is a map and you want to save it in the new position, you would have to resample it first. Resampling to create a new map is necessary since the original map would just show up in its old position if you save and reopen without resampling. This issue is discussed in the bottom part of this page: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 25, 2023, at 6:14 AM, Leonardo Talachia Rosa via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera team, I hope you are well.
I am processing a phage dataset which presents D5 pseudossymetry. The C5 axys is aligned to the z axys. I would like to rotate the map 90 degree in the z axys, so that Z axys now separate the molecule in a C2 pseudosymmetry, in order to play with some symmetry relaxation features to refine differences in the two map vortexes. Is there a way in chimera to rotate the map in relation to the xyz axys? The way I see, all rotate commands I know rotate the axys themselves alongside the map.
Thank you for your time, Kind wishes, Leonardo
Hi Leonardo,
As Elaine said, rotating the view in ChimeraX does not change what is saved in the map (*.mrc) file. The data needs to be rearranged in the 3D array. That can be done with the ChimeraX "volume resample" command (in Chimera it is called vop resample) but that interpolates the data on a new grid, and it would be better to just rotate the 3D data array so you don't get interpolation errors. I made a ChimeraX command to do that "volume rotate_90" available on the ChimeraX Recipes web site.
https://rbvi.github.io/chimerax-recipes/rotate_90/rotate_90.html
We no longer develop Chimera so I provide this for ChimeraX.
Tom
On Jan 25, 2023, at 6:14 AM, Leonardo Talachia Rosa via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera team, I hope you are well.
I am processing a phage dataset which presents D5 pseudossymetry. The C5 axys is aligned to the z axys. I would like to rotate the map 90 degree in the z axys, so that Z axys now separate the molecule in a C2 pseudosymmetry, in order to play with some symmetry relaxation features to refine differences in the two map vortexes. Is there a way in chimera to rotate the map in relation to the xyz axys? The way I see, all rotate commands I know rotate the axys themselves alongside the map.
Thank you for your time, Kind wishes, Leonardo
--
Leonardo TALACHIA ROSA, PhD PostDoctoral Researcher Microbiology and Structural Biology Instituto de Química, Universidade de São Paulo - IQ-USP Av. Prof. Lineu Prestes, 748 - Butantã, São Paulo - SP
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Leonardo Talachia Rosa -
Tom Goddard