Hi Jianhao, The problem is simply that one of your maps has center at 0,0,0 and the other does not. The “Center” button the Volume Viewer dialog does not fix this — it simply center the map in the view window but does not move it in the scene (the scene origin is not the same as the center of the window). The Center button on the Surface Color dialog sets the center for radial color choosing it to be the center of the volume surface. That is not perfect and it would be better to adjust the map so its center of symmetry is really at 0,0,0. To do this use can use the Volume Viewer menu Features / Coordinates and adjust “Origin Index” to be the grid point where the center of symmetry is located (often the middle grid point of the map, e.g. 50 50 50 if the map size is 100). Tom

On Sep 15, 2017, at 9:08 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Jianhao, If you color by radius it needs to know the point of reference for the coloring, i.e. the “origin” coordinates in the Surface Color dialog. It sounds like you just left that as 0 0 0 and instead changed the map center to 0 0 0 with Volume Viewer. The simpler way is to just click the “center” button next to the “origin” field in Surface Color and it will automatically fill in the origin values with the coordinates of the center of map, if that is what you want to use as the point of reference.

If you’re using command “scolor” with “geometry radial" to do the coloring, there is a “center’ option to specify the point of reference. There is no option to automatically use the center of the map, but you could use the Surface Color dialog to find that out. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#radial>

However, if you wtill wanted to change the map coordinates instead of simply specifying the center for coloring, it can be done with the “volume” command, see the “origin” and “originIndex” options <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions>

The volume command does most of the things that are in the Volume Viewer GUI. You can search that page for various things you want to do with commands.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On Sep 14, 2017, at 6:19 PM, C.J. <biocjh@gmail.com> wrote:

Hi specialists,

I want to color a map by radius. But for some maps, it failed. I found that that "center"(Volume Viewer -> Features -> Coordinates) button(not the one at bottom of Volume Viewer dialog) can center a map to color by radius. Is there a command-line to do that function? And why some maps need to be center before color by radius? I have 2 C1 map with spherical shape reconstructed from the same data, but one need to and the other one needn't. Thank you in advances!

Best regards! Jianhao

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Thank you all! My maps is imposed with a C1 symmetry. So I just want to know a coarse center. Regards! Jianhao 2017-09-16 2:13 GMT+08:00 Elaine Meng <meng@cgl.ucsf.edu>:

Hi Jianhao, That “center” button in the Coordinates section fills in the origin index as the center of your map, with values (grid dimensions - 1)/2. I had a test map with dimensions 35 26 30 and when I clicked that button it filled in the origin index values as 17 12.5 14.5. To do the same thing as that button, you could figure out the values from your map’s grid dimensions and specify them with the “originIndex” option of the “volume” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ volume.html#dimensions>

However, as Tom mentioned, the center of the map grid might not be exactly the same as center of symmetry. If they’re different and you know the grid indices of the center of symmetry, you would use those values instead. Chimera doesn’t have a way to figure them out automatically. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

-- Best regards! C.J.