[Chimera-users] Fit model and density map
meng at cgl.ucsf.edu
Thu Dec 26 10:31:48 PST 2019
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
…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 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 at 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 at 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,
>> 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.
>> 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 at yale.edu> wrote:
>>> Is there any one knows how to fit the density map to this red model?
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