[Chimera-users] Electron density map around selected residues
wnovak at brandeis.edu
Wed Jul 23 09:05:44 PDT 2008
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 Pufall
> UC San Francisco
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
Walter R.P. Novak, Ph.D.
Rosenstiel Basic Medical Research Center
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405
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