<div dir="auto"><div>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.</div><div dir="auto"><br></div><div dir="auto">Multiple the segmented mrc file with the original map and then use the output file to fit the pdb to.</div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><br><br><div class="gmail_quote" dir="auto"><div dir="ltr" class="gmail_attr">On Thu, Dec 26, 2019, 10:40 AM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Wangbiao,<br>
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). <br>
<br>
I see that Amira mesh is listed together with map formats (e.g. with the Chimera “listfiletypes” startup option) and in this table<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume" rel="noreferrer noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume</a>><br>
…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.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Dec 26, 2019, at 10:00 AM, Guo, Wangbiao <<a href="mailto:wangbiao.guo@yale.edu" target="_blank" rel="noreferrer">wangbiao.guo@yale.edu</a>> wrote:<br>
> <br>
> Dear Elaine: <br>
> 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. <br>
> <br>
>> On Dec 24, 2019, at 9:57 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" rel="noreferrer">meng@cgl.ucsf.edu</a>> wrote:<br>
>> <br>
>> Hi Wangbiao,<br>
>> 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, <br>
>> <<a href="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" rel="noreferrer noreferrer" target="_blank">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</a>><br>
>> 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.<br>
>> Best,<br>
>> Elaine<br>
>> -----<br>
>> Elaine C. Meng, Ph.D. <br>
>> UCSF Chimera(X) team<br>
>> Department of Pharmaceutical Chemistry<br>
>> University of California, San Francisco<br>
>> <br>
>> <br>
>>> On Dec 24, 2019, at 1:49 PM, Guo, Wangbiao <<a href="mailto:wangbiao.guo@yale.edu" target="_blank" rel="noreferrer">wangbiao.guo@yale.edu</a>> wrote:<br>
>>> <br>
>>> Is there any one knows how to fit the density map to this red model?<br>
>>> <br>
<br>
<br>
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</blockquote></div></div></div>