Dear colleagues, Could you advise on how to crop the map to the new 3D box size and save those changes? Thank you. Sincerely, Dmitry
Hi Dmitry, You could create a copy of the map but only a region using "volume copy" with the "subregion" option to specify grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#copy> Or, to save a map file with the smaller region, the "save" command allows specifying the map "region" by grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> (The current documentation also suggests you could also use a name for the region instead of the ranges, but I suspect that it is incorrect, so disregard that part.) If you are using the "crop" mouse mode to interactively crop the map box, look in the Log: it will show a "volume" command with the "region" giving the indices you could use in the "volume copy" or "save" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:47 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Could you advise on how to crop the map to the new 3D box size and save those changes?
Thank you.
Sincerely, Dmitry
thank you, Elaine, It worked but the newly created map was shifted away from the Origin one. What I am aiming for is to crop the Original map together with the box size, but the new smaller map with the smaller box size was still in the center. In the sketch below I need to get the orange cylinder (168x168x168) from the Origin blue cylinder (384x384x384). So when I open the orange and the blue maps both cylinders overlap. Is there such an option in ChimeraX? Thank you in advance. Sincerely, Dmitry [cid:c0c275de-798d-4450-9a2c-66afdb5d5c17] ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 25 October 2023 17:34 To: Dmitry Semchonok <semchonok@gmail.com> Cc: ChimeraX <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] crop the map Hi Dmitry, You could create a copy of the map but only a region using "volume copy" with the "subregion" option to specify grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#copy> Or, to save a map file with the smaller region, the "save" command allows specifying the map "region" by grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> (The current documentation also suggests you could also use a name for the region instead of the ranges, but I suspect that it is incorrect, so disregard that part.) If you are using the "crop" mouse mode to interactively crop the map box, look in the Log: it will show a "volume" command with the "region" giving the indices you could use in the "volume copy" or "save" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:47 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Could you advise on how to crop the map to the new 3D box size and save those changes?
Thank you.
Sincerely, Dmitry
Hi Dmitry, When I tried it (e.g. volume copy) the region was exactly superimposed on the same part of the original map, see attached image. Maybe you moved one map separately from the scene, such as to fit it to another? If so, you could try applying its transformation to the other one with "view position" using the "sameAsModels" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 9:54 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
thank you, Elaine,
It worked but the newly created map was shifted away from the Origin one.
What I am aiming for is to crop the Original map together with the box size, but the new smaller map with the smaller box size was still in the center. In the sketch below I need to get the orange cylinder (168x168x168) from the Origin blue cylinder (384x384x384). So when I open the orange and the blue maps both cylinders overlap.
Is there such an option in ChimeraX?
Thank you in advance.
Sincerely, Dmitry
<image.png> From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 25 October 2023 17:34 To: Dmitry Semchonok <semchonok@gmail.com> Cc: ChimeraX <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] crop the map
Hi Dmitry, You could create a copy of the map but only a region using "volume copy" with the "subregion" option to specify grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#copy>
Or, to save a map file with the smaller region, the "save" command allows specifying the map "region" by grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
(The current documentation also suggests you could also use a name for the region instead of the ranges, but I suspect that it is incorrect, so disregard that part.)
If you are using the "crop" mouse mode to interactively crop the map box, look in the Log: it will show a "volume" command with the "region" giving the indices you could use in the "volume copy" or "save" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:47 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Could you advise on how to crop the map to the new 3D box size and save those changes?
Thank you.
Sincerely, Dmitry
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
P.S. Make sure you use the grid indices, not just the size, to specify the copy subregion or save region. In my image, the original map is emdb 25428 (300 x 300 x 300) and the copy command was volume copy #1 subregion 150,93,0,236,184,131
On Oct 25, 2023, at 10:55 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, When I tried it (e.g. volume copy) the region was exactly superimposed on the same part of the original map, see attached image.
Maybe you moved one map separately from the scene, such as to fit it to another? If so, you could try applying its transformation to the other one with "view position" using the "sameAsModels" option:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<subregioncopy.png>
On Oct 25, 2023, at 9:54 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
thank you, Elaine,
It worked but the newly created map was shifted away from the Origin one.
What I am aiming for is to crop the Original map together with the box size, but the new smaller map with the smaller box size was still in the center. In the sketch below I need to get the orange cylinder (168x168x168) from the Origin blue cylinder (384x384x384). So when I open the orange and the blue maps both cylinders overlap.
Is there such an option in ChimeraX?
Thank you in advance.
Sincerely, Dmitry
<image.png> From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 25 October 2023 17:34 To: Dmitry Semchonok <semchonok@gmail.com> Cc: ChimeraX <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] crop the map
Hi Dmitry, You could create a copy of the map but only a region using "volume copy" with the "subregion" option to specify grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#copy>
Or, to save a map file with the smaller region, the "save" command allows specifying the map "region" by grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
(The current documentation also suggests you could also use a name for the region instead of the ranges, but I suspect that it is incorrect, so disregard that part.)
If you are using the "crop" mouse mode to interactively crop the map box, look in the Log: it will show a "volume" command with the "region" giving the indices you could use in the "volume copy" or "save" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:47 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Could you advise on how to crop the map to the new 3D box size and save those changes?
Thank you.
Sincerely, Dmitry
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Dmitry, If you display only part of a map, for example by using the crop map mouse mode, or a command like volume #1 region 50,50,50,100,100,100, then if you use the ChimeraX save command it only saves that shown region. save mappiece.mrc model #1 You don't have to specify the "region" option when saving, and you don't need to use the volume copy command to save the cropped map. Tom
On Oct 25, 2023, at 9:34 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, You could create a copy of the map but only a region using "volume copy" with the "subregion" option to specify grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#copy>
Or, to save a map file with the smaller region, the "save" command allows specifying the map "region" by grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
(The current documentation also suggests you could also use a name for the region instead of the ranges, but I suspect that it is incorrect, so disregard that part.)
If you are using the "crop" mouse mode to interactively crop the map box, look in the Log: it will show a "volume" command with the "region" giving the indices you could use in the "volume copy" or "save" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:47 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Could you advise on how to crop the map to the new 3D box size and save those changes?
Thank you.
Sincerely, Dmitry
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Elaine and Tom, Thank you for the new knowledge about the ChimeraX feature. It is very useful. Using your instructions, I managed to cut the appropriate piece of the map. Just a small additional question - when I select the box size, I want to keep it similar to the center of mass grid index. But sometimes center of mass grid index of the map does not have integer values. So, when applying the script where the numbers are not integer, e.g., volume copy #1 subregion 108,108,108.1,276,276,276.1 I am getting an error Must specify 6 comma-separated integers, got 108,108,108.1,276,276,276.1 Is there a walk-around rather than setting or removing the number after the dot? Many thanks again! Sincerely, Dmitry ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: 25 October 2023 19:19 To: Dmitry Semchonok <semchonok@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] crop the map Hi Dmitry, If you display only part of a map, for example by using the crop map mouse mode, or a command like volume #1 region 50,50,50,100,100,100, then if you use the ChimeraX save command it only saves that shown region. save mappiece.mrc model #1 You don't have to specify the "region" option when saving, and you don't need to use the volume copy command to save the cropped map. Tom
On Oct 25, 2023, at 9:34 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, You could create a copy of the map but only a region using "volume copy" with the "subregion" option to specify grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#copy>
Or, to save a map file with the smaller region, the "save" command allows specifying the map "region" by grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
(The current documentation also suggests you could also use a name for the region instead of the ranges, but I suspect that it is incorrect, so disregard that part.)
If you are using the "crop" mouse mode to interactively crop the map box, look in the Log: it will show a "volume" command with the "region" giving the indices you could use in the "volume copy" or "save" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:47 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Could you advise on how to crop the map to the new 3D box size and save those changes?
Thank you.
Sincerely, Dmitry
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Dmitry, The data values are located only at the grid points, with integer indices. So even if you draw the box slightly different from where the grid points are, there is no data there. You can resample a map on a different grid to get values at different positions, but it is done by interpolation, which decreases resolution (loses the exact original data values). <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#resample> Elaine
On Oct 25, 2023, at 12:52 PM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine and Tom,
Thank you for the new knowledge about the ChimeraX feature. It is very useful.
Using your instructions, I managed to cut the appropriate piece of the map.
Just a small additional question - when I select the box size, I want to keep it similar to the center of mass grid index. But sometimes center of mass grid index of the map does not have integer values. So, when applying the script where the numbers are not integer, e.g., volume copy #1 subregion 108,108,108.1,276,276,276.1 I am getting an error Must specify 6 comma-separated integers, got 108,108,108.1,276,276,276.1 Is there a walk-around rather than setting or removing the number after the dot?
Many thanks again!
Sincerely, Dmitry From: Tom Goddard <goddard@sonic.net> Sent: 25 October 2023 19:19 To: Dmitry Semchonok <semchonok@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] crop the map
Hi Dmitry,
If you display only part of a map, for example by using the crop map mouse mode, or a command like volume #1 region 50,50,50,100,100,100, then if you use the ChimeraX save command it only saves that shown region.
save mappiece.mrc model #1
You don't have to specify the "region" option when saving, and you don't need to use the volume copy command to save the cropped map.
Tom
On Oct 25, 2023, at 9:34 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, You could create a copy of the map but only a region using "volume copy" with the "subregion" option to specify grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#copy>
Or, to save a map file with the smaller region, the "save" command allows specifying the map "region" by grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
(The current documentation also suggests you could also use a name for the region instead of the ranges, but I suspect that it is incorrect, so disregard that part.)
If you are using the "crop" mouse mode to interactively crop the map box, look in the Log: it will show a "volume" command with the "region" giving the indices you could use in the "volume copy" or "save" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:47 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Could you advise on how to crop the map to the new 3D box size and save those changes?
Thank you.
Sincerely, Dmitry
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Dmitry Semchonok -
Elaine Meng -
Tom Goddard