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