The segmented Amira file when converted to mrc should be similar to a binary. E.g. every voxel not highlighted would have the value 0, the the first label field will have the value 1, the second label field 2 etc. Multiple the segmented mrc file with the original map and then use the output file to fit the pdb to. On Thu, Dec 26, 2019, 10:40 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Wangbiao, I’m guessing that an Amira mesh file may just describe a surface or surfaces, rather than a map (3D grid with values at every point).
I see that Amira mesh is listed together with map formats (e.g. with the Chimera “listfiletypes” startup option) and in this table <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> …but it may be because they are generally used together. If my guess is correct, it may not be interchangeable with or equivalent to those data types.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 26, 2019, at 10:00 AM, Guo, Wangbiao <wangbiao.guo@yale.edu> wrote:
Dear Elaine: Thank you very much. The red model is the Amira segmentation file, I changed it to mrc file. I want to fit the model with density map. I don’t know why I cannot save the model as map.
On Dec 24, 2019, at 9:57 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Wangbiao, I don’t know what that red thing is. Is it just a surface, or is it another map that happens to have an isosurface displayed? (What kind of file did it come from?) You can fit a map to another map, < https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.uc...
but there isn’t a tool to fit a map to a surface… it’s just an empty shell. Maybe you could somehow first make a new map based on that surface (e.g. 1 inside 0 outside) and then try to fit to that, but I don’t know if that really makes sense or would even work. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 24, 2019, at 1:49 PM, Guo, Wangbiao <wangbiao.guo@yale.edu> wrote:
Is there any one knows how to fit the density map to this red model?
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