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
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). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#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": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> I hope this helps, Elaine ---------- 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
Hi Hernando, This is a bug. In Chimera 1.6 and the daily builds if you draw a volume subregion selection box (green outline box) using one map and then use it to crop another map which has different grid bounds or different grid spacing then the cropped region doesn't match the box bounds. I've fixed it in tonight's Chimera daily build. In the broken Chimera versions you can avoid the problem by making both maps have identical grids using the vop resample command, for example, "vop resample #1 ongrid #0". Thanks for reporting this bug. Tom -------- Original Message -------- Subject: [Chimera-users] density maps & sub-region selection. From: Hernando J Sosa To: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Date: 10/16/12 9:52 AM
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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participants (3)
-
Elaine Meng -
Hernando J Sosa -
Tom Goddard