[Chimera-users] Extract a chain in cryo-EM map

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 25 11:15:57 PST 2019

Dear Bahareh Behkamal,
You can always save a map from the Volume Viewer tool (in that tool’s menu File… Save map as) or with the “volume” command


However I guess the main question is how to edit the map to get only the part of it that you want.  If you want to get a part that is near to some atoms, you also have to open the atomic model.  If the fit is not already available, you would also have to fit the atomic model to the map yourself.  However, I see that the fit atomic model is already available:

I used Chimera menu: File… Fetch by ID, choice “EMDB & fit PDBs” and entered 5030 to fetch.  However, the fit atomic structure. PDB 4v68, does not have a chain R… for example, look in Chimera menu: Select… Chains…[list of chains]. You have to figure out which chain(s) you actually want.

Then use command “vop zone” to make a new edited map that only keeps the values close to that chain.  For example, if the atoms are open as model #0 and map is #0.1, and you wanted the map within 5 Angstroms of chain AG, command could be something like:

vop zone #0.1 #0:.AG 5

Therre are other options to the command, see

The “vop zone” command makes a new map which you could then save as described at the top of this message.

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

> On Nov 24, 2019, at 3:56 PM, bahareh behkamal <b.behkamall at gmail.com> wrote:
> Dear secretariat,
> Would you please say to me how I can extract a chain in the cryo-EM map and save it separately as a ".mrc" file?
> For example, I need to select chain R in protein EMD-5030 which is attached at the following link.
>  EMD-5030.map
>  I am grateful if you could help me regard this issue.

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