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

[Tom Goddard]

Hi Andre,

  The Segger segmentation tool was written by Greg Pintilie, not by the UCSF ChimeraX team.  I moved part of it from Chimera to ChimeraX hoping to convince Greg to switch from Chimera to ChimeraX, but so far no luck.  Chimera has not been developed for 5 years except for critical fixes so it is too bad most of the Segger tools are not in ChimeraX.

	Tom


> On Feb 4, 2022, at 11:40 AM, Andre LB Ambrosio via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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 <mailto: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 <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 <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 <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 <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
> 
> <Screen Shot 2022-02-04 at 8.47.59 AM.png>
> 
> 
>> On Feb 4, 2022, at 7:55 AM, Andre LB Ambrosio via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto: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 <http://www.ifsc.usp.br/alba>
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