[Chimera-users] Electron density map around selected residues

Walter Novak wnovak at brandeis.edu
Wed Jul 23 09:05:44 PDT 2008

Hi Miles,

You can use the zone tool in the volume viewer (Features->Zone), it  
works great for depicting the electron density for a given area. I  
first hide the density by clicking on the eyeball in the volume  
viewer, then select the residues I want and click the zone button.  
Clicking the eyeball again shows the density in only the selected  
zone. You can give a zone radius too.


On Jul 23, 2008, at 3:32 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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Walter R.P. Novak, Ph.D.
Postdoctoral Fellow
Rosenstiel Basic Medical Research Center
Brandeis University
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405

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