[Chimera-users] Structure is not fitted and map has multiple duplicates in Coot

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 20 13:15:59 PDT 2019

Hi Ahmad,
Coot may do some symmetry operations to show additional copies, but you’d have to ask the Coot people about it since we don’t know the details of that program.

Saving a map in Chimera does not save any rotations that were applied, since the map format does not have anywhere to put that information.  This is a commonly asked question in Chimera.  Either you have to fit structures to map and then just save the atomic structures (PDBs) in the fitted positions, or if you want the density to be rotated you have to resample the map on a new grid with “vop resample” and then save the resampled map.

See the help section “Saving Maps after Fitting," which has additional links for more details:

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

> On Mar 20, 2019, at 12:46 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> I have a cryo-EM map that I want to segment. I have structures surrounding the density of interest from all sides. I did a molmap in chimera and subtracted everything the molmap. I then cleaned the excess density around my protein using volume eraser. 
>  Now the map that I get opens fine in Chimera. But I tried to open a model and my density in Coot, the screenshot is what I got:
> 1) the structure is not fitted
> 2) the density appears to have multiple copies of my proteins, it's supposed to be only one unit there
> What is wrong here exactly, I'm suspecting it's the volume eraser! Is there a better way to segment the density given how I have atomic models for all the surrounding densities, but not the density of interest? 
> Regards. 
> <coot_duplicates.PNG>

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