[Chimera-users] fitting open conformation (map)

Elaine Meng meng at cgl.ucsf.edu
Sat Feb 13 08:54:37 PST 2021

Hi Neha,
I'm not sure what would work best.  If you also have a PDB of the open conformation that is already in its map (map of the open conformation), then the easiest would probably be to superimpose the PDB of the closed conformation on the PDB of the open conformation.  There are several ways to superimpose PDBs, as discussed in this User Guide page, although probably the easiest would be the Matchmaker tool (In menu under Tools.. Structure Comparison):


Although you can try fitting a PDB or map of one conformation (e.g. closed) on the map of the other conformation (e.g. open), I don't know whether it would end up in the place that wanted or expected.  The tool to fit PDBs or maps in maps is menu: Tools... Volume Data... Fit in Map. 

 Also you would have to position the PDB or map to fit by hand in approximately the right place of the other map first, since that tool does local optimization.  For more details, click the links in the sentence "This usually involves interactive manipulation and toggling models between active and immovable states" in the Fit in Map help page linked above.

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

> On Feb 13, 2021, at 3:38 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:
> Hi Elaine,
> There is a cryo-EM structure of the spike trimer in closed conformation. I have downloaded pdb file and map files for the locked conformation. I am interested in aligning or mapping map of the open conformation (fitting pdb from closed conformation pdb on the map). Could you please advise how this can be achieved?
> Many thanks,
> Neha

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