[Chimera-users] Fit model and density map

[Elaine Meng]

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 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, 
>> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Ffitmaps%2Ffitmaps.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C6275cd9bc9384e8c922508d788e6212b%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128394297998014&sdata=W0Nw0%2Bwu2pdGYvP2WF29ZGrlUlMDUZs5%2BYZSfKm3ZZE%3D&reserved=0>
>> 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 at yale.edu> wrote:
>>> 
>>> Is there any one knows how to fit the density map to this red model?
>>>