Hi Grigory, The problem is your "vop new" map is not centered on the atomic model. While you could try to center it so it covers the atomic model I think it is easier to just crop the the non-cube map produced by molmap to be a cube of size 256 by 256 by 256. For example open 8q54 molmap #1 10 gridSpacing 0.6 > Opened 8q54 map 10 as #2, grid size 309,304,285, pixel 0.6, shown at level 0.123, step 1, values float32 volume #2 region 26,24,14,281,279,269 showOutline true save box.mrc model #2 The region option of the volume command lists the grid bounds imin,jmin,kmin,imax,jmax,kmax which I chose to make each dimension 256 grid points. You may need to use the molmap command edgePadding option to get a bigger molmap box around the structure. Instead of figuring out what numbers to type in the region command you can just use the Crop mouse mode in the Right Mouse toolbar and drag the faces of the molmap volume until you get it to a size of 256 cubed (size shown in the volume viewer panel). Yet another trick to get the cube map would be to use the "volume boxes" command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#boxes for instance in my example, I place a marker at the center of the molmap using the Toolbar Marker tab, click the Center mode, and right click the map to place a marker. That logs this command marker #3 position 133.9,134,133.1 color yellow radius 1 Then to extract a cube box of size 256 centered at that marker volume boxes #2 centers #3 isize 256 That didn't quite work giving a box size 256 x 256 x 247 because my molmap box was not big enough to cover so I would go back and use the molmap edgePadding option to have molmap create a bigger box around the atomic model. Tom 

On Aug 22, 2024, at 12:24 PM, Grigory Mechetin, Ph.D. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX developers, when I use the molmap command on grid ('molmap #1 10 onGrid #2', grid2 was created with' vop new size 256,256,256 gridSpacing 0.74' command ) I get half-map. How to get the full one?

When I use molmap without onGrid it generates the volume with non-equal grid size, but I need square 256^3 grid.

<image.png>

Best regards, Grigory Mechetin, PhD, MEMS, Duke University. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Thank you, Elaine and Tom, I'll try. I tried 'volume boxes' according to Tom's advice, it gave me the map of 256^3 according to ChimeraX log and volume viewer, but Cryosparc still doesn't accept it as cubic (ValueError: cannot reshape array of size 9436928 into shape (256,256,256). It accepted my 'half-map' before. Best, Grigory. ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, August 22, 2024 5:34 PM To: Grigory Mechetin, Ph.D. <grigory.mechetin@duke.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] molmap command question Hi Grigory, I guess the grid from map #2 in your example does not cover your molecule. When you use "volume new" (aka vop new) to make the grid, you need to also specify the "origin" and "gridSpacing" values needed to cover your molecule. This will probably take trial and error and you will need to show the outline box of that grid to make sure (command: volume showoutlinebox true). <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > After you get the grid that covers the molecule, then use "molmap" specifying that grid with "onGrid." 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 Aug 22, 2024, at 12:24 PM, Grigory Mechetin, Ph.D. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX developers, when I use the molmap command on grid ('molmap #1 10 onGrid #2', grid2 was created with' vop new size 256,256,256 gridSpacing 0.74' command ) I get half-map. How to get the full one?

When I use molmap without onGrid it generates the volume with non-equal grid size, but I need square 256^3 grid.

<image.png> Best regards, Grigory Mechetin, PhD, MEMS, Duke University.

Hi Grigory, That error with your 256^3 map makes me think the map isn't really of that size because 256 x 256 x 256 = 16777216. I guess it is possible your MRC file that ChimeraX saved is truncated. To test that I would just open the MRC map you saved with ChimeraX in ChimeraX and see if opens and reports its size as 256^3. And you can also just look at the MRC file size. If it is 256^3 with 32-bit floating point values as produced by molmap then it should be about 64 Mbytes in size. Is the file that size? Tom

On Aug 23, 2024, at 7:50 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Grigory,

This sounds more like a cryosparc issue than a ChimeraX issue per se - may be worth posting to the CryoSPARC forums: https://discuss.cryosparc.com/

Cheers Oli

...

On Aug 23, 2024, at 10:45 AM, Grigory Mechetin, Ph.D. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thank you, Elaine and Tom, I'll try. I tried 'volume boxes' according to Tom's advice, it gave me the map of 256^3 according to ChimeraX log and volume viewer, but Cryosparc still doesn't accept it as cubic (ValueError: cannot reshape array of size 9436928 into shape (256,256,256). It accepted my 'half-map' before.

Best, Grigory. From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Thursday, August 22, 2024 5:34 PM To: Grigory Mechetin, Ph.D. <grigory.mechetin@duke.edu <mailto:grigory.mechetin@duke.edu>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] molmap command question

Hi Grigory, I guess the grid from map #2 in your example does not cover your molecule.

When you use "volume new" (aka vop new) to make the grid, you need to also specify the "origin" and "gridSpacing" values needed to cover your molecule. This will probably take trial and error and you will need to show the outline box of that grid to make sure (command: volume showoutlinebox true). <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >

After you get the grid that covers the molecule, then use "molmap" specifying that grid with "onGrid."

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 Aug 22, 2024, at 12:24 PM, Grigory Mechetin, Ph.D. via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:

Dear ChimeraX developers, when I use the molmap command on grid ('molmap #1 10 onGrid #2', grid2 was created with' vop new size 256,256,256 gridSpacing 0.74' command ) I get half-map. How to get the full one?

When I use molmap without onGrid it generates the volume with non-equal grid size, but I need square 256^3 grid.

<image.png> Best regards, Grigory Mechetin, PhD, MEMS, Duke University.

_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto: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/