[chimerax-users] extraction of certain cryo-em density

[Christian Tüting]

Hi Dmitry,

just for the records of the mailing list (as somebody have the same issue):

Load map and model.

Test your selection (this step is not needed, but helps if the selection includes multiple parts)
# hide all atoms
hide atoms
# show your selection. The model is #2, you want to only select chlorophyll from chain A

show #2/A:BCL

This should display just your molecule/residue/ligand of interest.
For the selection syntax:

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html

Now create a new map, just from your molecule
volume zone #1 nearAtoms #2/A:BCL newMap true

One can include also the range parameter (default 3.0), e.g. if the molecule placement is a bit unsure and you want to refine it in there.

Now, just save the new map by
save mapZone.mrc #3


If you try multiple volume zones, you might need to correct the id.

Best
Christian


>>> "Dmitry A. Semchonok via ChimeraX-users" <chimerax-users at cgl.ucsf.edu> 02/08/22 12:42 PM >>>
Dear colleagues,


I have a cryo-em map and a model.


I would like to extract some the cryo-em density around certain fitted model.


For example I have Chl molecule fitted into the correspondent cryo-em density. 
And I want to extract this certain Chl only out of the whole structure.






How can I do that?






Kind regards,
Dmitry
 
Sent from Mail for Windows
 


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