[Chimera-users] Question about electron density map

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 4 10:32:34 PDT 2019

Hi Bixia,
If you are sure that this atomic structure is supposed to fit with this map, maybe it is because the fitting is only local optimization and it is too far from the correct position to find it. Before fitting you could try to get the approximate position yourself manually, by freezing one model and moving the other.  You can freeze/unfreeze using the “A” checkboxes in Model Panel (open from Favorites menu).

Activation (“A” checkboxes) for motion:

Assuming the atoms and map are in the right relationship to each other after fitting, then you can select some atoms and show only the part of the map that is close to those atoms, using the zone function in Volume Viewer.  In the Volume Viewer menu, Features… Zone as described here.

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

> On Oct 4, 2019, at 10:22 AM, Zhang, Bixia <bixia.zhang at wsu.edu> wrote:
> Dear Developer,
> I want to have a figure of my ligand only and its electron density, and I used my protein mtz file to generate a CCD4 map in phenix and then open in chimera. I tried fit in map but it does not fit well. Could you please help me out? And after I have the electron density, how to hide the backbone electron density? Thanks a lot!
> Best,
> Bixia

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