[Chimera-users] Electron density map around selected residues

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 23 09:09:16 PDT 2008

Hi Miles,
Sure, you can limit the display to a zone around selected atoms.  In  
Volume Viewer, choose Features... Zone.  Select the atoms,  click  
Zone.  You can then move the slider to change the zone radius.  This  
affects the "active" data set, the one with the highlighted name in  
the Volume Viewer dialog.  If you have more than one density map, just  
click on the histogram for the other one to make it the active set and  
click Zone again.  The only tricky thing is that moving the slider  
only adjusts one zone at a time, but you can switch back and forth by  
clicking the histograms.  It is fine to deselect the atoms - it  
"remembers" which atoms were selected when you clicked Zone.

I know you work in the same building as we do - feel free to stop by  
my office if any of this is unclear!
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 23, 2008, at 12:32 AM, Miles Pufall wrote:

> Hello -
> I have a couple of structures depicting a complex where the function  
> of a loop appears to be important, depending on conditions.  An  
> overlay of structures solved under these two conditions shows subtle  
> differences, but an examination of omit maps for this loop overlap  
> where the model is built, but show quite different extra density,  
> suggesting different alternate conformations.  I am trying to make a  
> figure of this loop with the 2fofc and omit maps overlaid on this  
> loop under the two conditions.  The figure, with a model and two  
> electron density maps, can get messy.  I would like to show just the  
> electron density surrounding just the loop.  Can you recommend a way  
> to do this in chimera?
> Thanks -
> Miles
> Miles Pufall
> UC San Francisco

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