Hi Guillaume,

  One additional approach (used by the ChimeraX fitmap command "sequence" option) is to simulate a map from each atomic model you have already fit and then subtract that simulated map from the experimental map.  Here's an example of an 8.2 Angstrom resolution gamma-tubulin complex with some proteins at the right (blue surface) that have not been fit.

open 18666 from emdb
open 8qv3
molmap #2 8.2
volume subtract #1 #3 minrms true

The "minrms true" option is key and says to subtract the second map after scaling it to minimize the residuals, since the simulated and experimental maps are not using the same intensity scale.

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract

    Tom

8qv3.png

On Apr 24, 2024, at 12:58 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Guillame,
You can make a map with "volume zone" and then subtract the zone from the original map with "volume subtract"  

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract>

Or you can use "volume mask" to zero out parts inside or outside of a surface
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask>

You can place markers manually at map density maxima, see the Marker Placement tool:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html>

...and associated mouse modes
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markers.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 24, 2024, at 12:44 PM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

With `volume zone` I can show the parts of a map close to an atomic model. Is there a way to do the opposite, i.e. show only the parts of a map that don’t enclose any atoms?

This would be already very helpful only as a visualization. But even better would be a way to build a list of markers at the centroids of such unmodeled blobs, to easily navigate to them. Or maybe this is too narrow in scope and better left to ISOLDE? (Sorry Tristan… more feature suggestions…).

Thank you,

Guillaume


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