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@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.ht...
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@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
