[Chimera-users] Fit model and density map

[Tom Goddard]

Yes, the Amira mesh is just a surface (a set of triangles), not a density map.  Chimera has no way to fit a surface to a density map.  You could convert the surface to a density map with all ones inside the surface and all zeros outside using the Chimera mask command

   https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html

for example

	mask ones #1

where the Amira mesh is model #1.  If you are trying to fit a PDB to the density within this surface you could instead use the mask command on the original EM density

	mask #0 #1

where #0 is the original density and #1 is the Amira mesh to get just the density within the surface, then fit the PDB in the resulting masked density as Karen suggested.

	Tom


> On Dec 27, 2019, at 7:44 AM, Guo, Wangbiao <wangbiao.guo at yale.edu> wrote:
> 
> 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?
>>>>> 
>> 
> 
> 
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