Dialing,
狢 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. 泎ut it may just be a matter of
personal taste.

-Nat
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb