[chimerax-users] Extract densities option not available on Segment Map

[Andre LB Ambrosio]

Dear Elaine, many thanks for this.
Sorry for overlooking the help page.
I ended up installing Chimera to use the "extract densities" option, as I
had difficulties matching the exact box dimensions of the new map to that
of the original map when using the volume mask command.
I can move forward with local refinement now!
Thank you again.

Em sex., 4 de fev. de 2022 às 13:55, Elaine Meng <meng at cgl.ucsf.edu>
escreveu:

> Hi Andre,
> According to the ChimeraX help page for the Segment Map tool, menu
> "Regions... Extract densities" is not yet implemented:
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html#menu-regions>
>
> However, I think you can find the model number of the surface (group) that
> you want by looking in the Model Panel, and then extract that part of the
> density map using the "volume mask" command:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask>
>
> For example, in the attached screen shot of a fake example I made up, I
> have several segmentation regions. The overall segmentation model is #3 and
> I can see that the one I have selected is the green blob in the middle,
> which is named 285 in the model panel and is model #3.1.  The density map
> is #2.  So (for example) to get density of map #2 inside surface #3.1 to
> create new map model #5 I can use command
>
> volume mask #2 surfaces #3.1 modelId #5
>
> There are other options of the command, see the link above.  Then you can
> save map #5 to a file with "save" command:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
>
> The alternative is to use Segger in Chimera, where I believe that the
> extract densities option in the Regions menu is implemented:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html#menu-regions
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> On Feb 4, 2022, at 7:55 AM, Andre LB Ambrosio via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear all, probably a silly question:
> I want to generate a mask o ChimeraX to use later on a local refinement
> job elsewhere.
> I managed to segment the cryoEM map and group the regions of interest.
> However, the "Extract densities" option is unavailable on the "Regions"
> menu.
> Likewise, these are unavailable on "Other tools" shortcuts options:
> Extract, iSeg, ProMod, and ModelZ.
> Please, what am I missing?
> I appreciate any help you can provide.
>
>
>

-- 
Andre LB Ambrosio
Associate Professor, IFSC/USP - Brazil
www.ifsc.usp.br/alba
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