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

[bahareh behkamal]

Hi,
I am really grateful for fast and comprehensive response.

*Regards,*
Bahareh Behkamal
Ph. D. Candidate of Computer Engineering
Dept. of Computer Engineering - System Software
Researcher in Structural Bioinformatics
*Ph. D visiting student in Politecnico di Torino, Italy*
Dept. of Applied Science and Technology




On Mon, Nov 25, 2019 at 10:45 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html
> >
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output
> >
>
> 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:
> <https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-5030>
>
> 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.
> <https://www.rcsb.org/structure/4v68>
>
> 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
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>
>
> 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
> -----
> 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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