[Chimera-users] electron density map superimposed on protein model

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 27 16:29:55 PDT 2019

Hi Jenaro,
It shouldn’t matter that you moved the structure in between opening the files.  However, to make sure, you can just close both and reopen both without moving in between.  It will probably be just as displaced.  Even though the map “goes with” the atomic coordinates, it may be that the deposited atomic coordinates are not overlaid with the map.  

I thought that the maps from EDS were superimposed with the corresponding structures, however, so also check that you have the correct PDB ID and that the map is really the one you want (2fo-fc or fo-fc).

Another possible situation is that they *are* aligned, but you would need to extend the map using crystal symmetry to cover all of the atoms.  Normally this would be done with the “vop cover” command but I see a previous post that the EDS server maps may not contain the needed symmetry information:

If they are really just not aligned:

You can fit PDB to a map with the Fit in Map tool (in menu under Tools… Volume Data).  

Then if you want to save the fitted position, you should save the PDB structure, not the map, as explained here.

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

> On Mar 27, 2019, at 4:15 PM, Jenaro Soto <jenaros at uci.edu> wrote:
> Hi Everyone, 
> I am new to Chimera and am still getting to know the program. So far I have found the tutorials helpful, but they don't seem to have the answer to this very specific question. 
> I want to know how I can overlay a protein structure and electron density map correctly. 
> I am currently analyzing a published structure and would like to look at the the electron density map superimposed on the protein model. I was able to fetch the electron density map by using the 'open edsID:PDB_ID' command. However,  it doesn't seem like my structure and the electron density are overlaid correctly. This might be because I moved the structure a lot before calling in the electron density map. 
> How can I have the electron density map overlaid to the structure correctly (like the author intended it to be).  
> Any tips will be appreciated. 
> Best, 
> Jenaro 

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