[Chimera-users] Fit model and density map

[Karen Davies]

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 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
> <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?
> >>>
>
>
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