Cutting out an asymmetric unit from the map
Hi!
I was wondering if there is a sequence of commands one could use to extract an asymmetric unit from the original map after roughly fitting the model into it. The positions of these extracted maps should of course be preserved and should on the same grid. One can then better fit the model in this extracted ASU density.
Thanks in advance for any guidance. Abhi
Hi Abhi, Well, with "volume zone" you can make a new map with zeroes beyond some cutoff distance of the atom positions. However, that seems a bit circular if the point is to fit the atoms again. I guess you could use a large-ish cutoff distance.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone
Since you fit the atoms into the map, the map grid would retain its original coordinates and the new edited map would just use that same grid. I.e., if I understand correctly, there isn't an issue of preserving the map position, since it was the atomic structure that was repositioned, not the map.
If the atomic structure is not occupying the entire asymmetric unit of the map (say there are other protein or nucleic acid chains also in the AU but explicitly present as atomic structures), however, the approach above would not be useful.
There are other ways to crop out parts of the map, such as by drawing a rectangular box manually (or specifying that region directly in a "save" map command) or using the Map Eraser tool to erase inside a sphere that can be moved with the mouse. See: https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#erase https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html
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 Apr 23, 2024, at 1:57 PM, Das, Abhinaba via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi!
I was wondering if there is a sequence of commands one could use to extract an asymmetric unit from the original map after roughly fitting the model into it. The positions of these extracted maps should of course be preserved and should on the same grid. One can then better fit the model in this extracted ASU density.
Thanks in advance for any guidance. Abhi
Hi Abhi,
The ChimeraX "volume zone" command will do this. For example,
open 8orh open 17125 from emdb volume zone #2 near #1 minimalBounds true save asym_unit.mrc model #2 open asym_unit.mrc
Here we open a PDB of the asymmetric unit for an EMDB map, then show the map just near the atomic model and use the "minimalBounds true" option so it crops the map bounds to contain that asymmetric unit. Then save that cropped part of the map to a new MRC file. The volume zone command will show just the map surface near atomic model, but the saved map will contain the full cropped box of map data and will preserve alignment with the original map.
Tom

On Apr 23, 2024, at 1:57 PM, Das, Abhinaba via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi!
I was wondering if there is a sequence of commands one could use to extract an asymmetric unit from the original map after roughly fitting the model into it. The positions of these extracted maps should of course be preserved and should on the same grid. One can then better fit the model in this extracted ASU density.
Thanks in advance for any guidance. Abhi _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
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Das, Abhinaba
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Elaine Meng
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Tom Goddard