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 wrote:

On Tue, Feb 28, 2012 at 3:44 PM, Dialing Pretty 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb