[Chimera-users] Fit model and density map

[Guo, Wangbiao]

Thank you very much, Elaine, may be I should try again.

> On Dec 26, 2019, at 1:31 PM, Elaine Meng <meng at 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
> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23volume&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cf586d0b0398e445f5c2108d78a31e047%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637129819141381522&sdata=Ykbx%2B3U8UTeqctsAxRzUjuWWsTmu1QzQp2ufpfmFrX4%3D&reserved=0>
> …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%7Cf586d0b0398e445f5c2108d78a31e047%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637129819141381522&sdata=4cEg0SRnXSv6OFqZSp0Tn34PiSd%2FwemOvB3p2Nqlu0w%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?
>>>> 
>