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

cube_8q54.png

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.
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