[Chimera-users] density maps & sub-region selection.

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 16 10:21:43 PDT 2012

Hi Hernando,
If you believe the map grids are the same (same number of points and spacing and are exactly superimposed), first make sure the Region bounds numbers are the same (in Volume Viewer, Features... Region bounds).

If they are the same but the boxes do not coincide, that suggests the grid of one map is displaced from the other. 

You might try resampling map A on the grid of map B, which will create a new map C derived from A but with exactly the same grid point locations as B.  Then the same Region bounds numbers should give the same box.

For resampling see command "vop resample":

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 16, 2012, at 9:52 AM, Hernando J Sosa wrote:

> Hi,
> I am trying to select  subregions in two density  maps using the subregion selection option in the volume viewer.   When selecting the  same subregion  different sub-volumes  in the two maps are selected (there is a displacement between the ROIs along  the Z axis) even though the two maps  are aligned to each other (or appear to be aligned in the display window).   Both maps are in the MRC format and both have a voxel size of 2A/pix. ?    Ideally what I want to do is to select equivalent regions of the two maps and then save them as new density maps.   How can I best do this?
> Thanks
> Hernando.
> UCSF Chimera version alpha 1.7 (build 36659)
> on Windows 7 64b

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