Dialing,
 I agree with Nat. Removing density from the map just to generate a nice figure is not a good idea. Why not generate an image showing the neighboring chains as well, or zoom in further?

Also, how did you calculate this map? Is it a low resolution, model-building map? Or is it a fully refined model-map?

Sincerely,
Kelly Daughtry

*******************************************************
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. Sands, Jr. Building
303 Research Drive
RM 250
Durham, NC 27710
P: 919-684-5178
*******************************************************


On Tue, Feb 28, 2012 at 6:53 PM, Nathaniel Echols <nechols@lbl.gov> wrote:
On Tue, Feb 28, 2012 at 3:44 PM, Dialing Pretty <hdc123hdc123@yahoo.com> wrote:
> Will you please give me some suggestion on how to edit the attached file so
> that those electron density not from the protein fragment can be erased? Or
> do you have other methods to produce high quality figure which just shows
> the fragment chain and the fragment eletron density?

You can use phenix.cut_out_density to do this.  The 'isomesh' command
in PyMOL also offers the ability to only draw mesh within a specified
distance of the selection of interest.

However, my impression was that this practice is somewhat frowned upon
- it is better to display the actual context of the map instead of
cutting out an idealized portion, which might be more pleasant to look
at but can often be misleading.  The image you attached is already
showing a very clean map that fits the peptides displayed very well; I
don't think it's necessary to clarify it further by reducing the
amount of information it conveys.  But it may just be a matter of
personal taste.

-Nat
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