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.
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