[Chimera-users] Density map segments and segment associated sequence extraction

[Elaine Meng]

Hi Ahmad,
That’s a rather broad question... almost a whole research project!   I can only answer generally, and even that is difficult because there are probably a dozen different approaches depending on how much is known about the overall structure, resolution of the map, amount and quality of atomic-structure data, etc.  You may want to look at the methods sections of papers that perform similar studies to learn about different strategies.

I haven’t published any such work myself, but based on my knowledge of Chimera, I can think of a few general approaches. Regardless, I believe you’d have to figure out ahead of time which pieces of structure to fit separately, and open them as separate PDB files.  Chimera is not going to figure out how to divide the structure for you.  For proteins open in Chimera, you can show their sequence using Favorites… Sequence in the menu, and then use the sequence window’s File menu to save fasta.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>

General approaches:

(A) segment-first: segment map based on the shape of the “blob” and then try to fit atomic-structure pieces into the individual segments of the map.  See tools “Segment Map” and “Fit to Segments”… the File menu of Segment Map allows saving the segmented parts of the map.

(B) fit-first: fit the atomic-structure pieces into the map and then split the map based on where the pieces are: see tools "Fit in Map" (and “fitmap” command has additional options for sequential fitting of multiple structures, which may be useful in your case), and for splitting the map based on the structures, "Color Zone.”

(C) mark, split, fit:  put a marker in the middle of each area of the map you want to fit separately, use Color Zone to split based on the marker positions, and then use Fit in Map.

These tools are all under Tools… Volume Data in the menu and each has a Help button to show detailed information. The Fit in Map help also links to the “fitmap” command information. There are also tutorials for Segment Map and Fit to Segments here:
<http://ncmi.bcm.edu/ncmi/software/segger/docs>

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 26, 2018, at 8:08 AM, Ahmad Abdelzaher <underoath006 at gmail.com> wrote:
> 
> Hello, 
> I have a density map that i'm trying to segment. I want to fit in my structure in the segmented map, and save each segment of the map as an independent mrc map, and each corresponding segment of the sequence as a fasta file.
> How can I do that?
> Kind regards