HI Elaine,

 Thanks but I do need to make a rectangular submap and need to do it within a script  (i.e. not using the GUI Subregion selection).   The script so far reads the coordinates from the model and the map information (step, origin, etc)

Thanks

Hernando




___________________________________
Hernando Sosa, PhD.                                                          
Dept. of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone (718) 430-3456
emai:  hernando.sosa@einsteinmed.edu
___________________________________


From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Tuesday, January 2, 2024 5:17 PM
To: Hernando J Sosa <hernando.sosa@einsteinmed.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Sub Volume map
 
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Hi Hernando,
Please see previous answer on the chimerax-users list (which  mentions both Chimera and ChimeraX).
<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimera-users%40cgl.ucsf.edu%2Fmessage%2FADCRCKYI4IIJLY4GK6GODJA3YWRW74E6%2F&data=05%7C02%7Chernando.sosa%40einsteinmed.edu%7C5ab3b574a2b34fa1f29708dc0be0b4e4%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C638398306939321160%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=DAN1%2B5y4oxlnYBPuuYS6xp17l%2B1etDNohtHj7L0TWMY%3D&reserved=0>

I should also mention you could consider drawing the region box interactively with the mouse in either program.

 In Chimera you could use the "Subregion selection" feature in the Volume Viewer dialog:
<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23mouseselect&data=05%7C02%7Chernando.sosa%40einsteinmed.edu%7C5ab3b574a2b34fa1f29708dc0be0b4e4%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C638398306939321160%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PLVAmSIS8uibPh8BZ45NfAIcKcETwcL7NMtGXwhioEg%3D&reserved=0>

In ChimeraX it is done with the "crop" mouse mode, which you can assign to the right mouse button by clicking the crop icon in the Right Mouse tab of the toolbar:
<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmousemodes.html&data=05%7C02%7Chernando.sosa%40einsteinmed.edu%7C5ab3b574a2b34fa1f29708dc0be0b4e4%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C638398306939321160%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bBiVZ%2FmOgBufRVH9q6DPeN2lCavKMVI1NlUog81y53A%3D&reserved=0>

In ChimeraX when you crop with the mouse it will report the equivalent command in the Log, which includes the region specification.

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 Jan 2, 2024, at 1:41 PM, Hernando J Sosa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear Chimera,
>
>
> I want to extract a submap around some parts of an atomic model that is aligned to the main map. For this I am using the volume region command, but I am running into a problem converting the atomic coordinates to voxel coordinates when the pixel size of the map is different from 1 and the map origin is not at 0,0,0.
>
> What should be the right formula to go from one set the coordinates to the other and  be able to get a submap in the right place?
>
> i.e.
> If a sub-volume were to be extracted at coordinates x1,y1,z1 and x2,y2,z2   of the atomic model
>
> what would be the volume coordinates to use in the command
>
> volume #mainmap region VX1, VY1, VZ1,  VX2, VY2, VZ2 assuming the map voxel size is Mapvsize and the map orig Orig is at cx,cy,cz.
>
> To  go from one set of coordinates to the other I have tried:
>
> MapCoord = (ModelCoord - Orig) / Mapvsize
>
> and
>
> MapCoord = (ModelCoord /Mapvsize) -  Orig
>
> None seems to extract the volume at the right place. The first one seems closer (??)
>
>
> Thanks
>
> Hernando
>
>
>
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