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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