[Chimera-users] Query on Cryo-EM map

Elaine Meng meng at cgl.ucsf.edu
Sun Oct 25 09:36:32 PDT 2015


Dear Aditya,
A density map and an atomic structure (set of atomic coordinates) are two different things.  Only atomic coordinates, not a map, can be saved as a PDB file.  You can only save a map file in some map formats.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#organization>

The second question has a similar answer.  A map isn’t marked automatically as to which parts are which proteins or chains.  You would have to segment the map then save the map part inside the segment of interest, or if there is an atomic structure, you could open the atomic structure and then fit it into the map. After fitting, one approach would be to color the atomic structure so that different parts (like different chains) are different colors, then use Color Zone to color the map to match the atoms and then to split the map by colors.

See Chimera tools: Segment Map, Fit to Segments, Fit in Map, Color Zone
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/fitsegments.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 24, 2015, at 10:31 AM, Aditya Padhi <adi.uoh at gmail.com> wrote:

> Dear Chimera Users,
> 
> I have a cryo-em map file and I would like to convert it into a PDB file. How can I do that? I tried saving the .pdb file but it throws an error saying “No model chosen to save”.
> 
> Another question, If I open a .map file of a protein complex in Chimera, how can I select a subregion (a particular chain) and colour the surface of that part differently? I am not able to select the chain when I upload the .map file.
> 
> Thank you,
> Aditya




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