[Chimera-users] difference electron density maps

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 17 08:22:36 PDT 2020

Hi Agata,
I guess you mean that the map has both positive and negative values, but when it first displays there is only one isosurface at a positive value.  

In the Volume Viewer dialog there is a histogram of the map values with a vertical bar marking the isosurface level.  You just Ctrl-click on the histogram to add another one.  You can drag the vertical bars (thresholds) horizontally on the histogram to whatever contour levels you want, positive and/or negative, change their colors, etc.

This is explained in the section about surface display with Volume Viewer:

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

> On Jul 17, 2020, at 3:13 AM, Butryn, Agata (DLSLtd,RAL,LSCI) <agata.butryn at diamond.ac.uk> wrote:
> Hello,
> I have been trying to display a difference electron density map in Chimera. The map was exported from Coot in a ccp4 format and contains both positive and negative peaks. When I load the map in Chimera only the positive peaks are displayed. Is there a way to display the negative peaks? 
> Many thanks and best wishes,
> Agata

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