<div>Dialing,</div><div>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?</div><div><br>
</div><div><div>Also, how did you calculate this map? Is it a low resolution, model-building map? Or is it a fully refined model-map?</div></div><div><br></div><div>Sincerely,</div><div>Kelly Daughtry</div><div><br clear="all">
*******************************************************<br>Kelly Daughtry, Ph.D.<br>Post-Doctoral Fellow, Raetz Lab<br>Biochemistry Department<br>Duke University<br>Alex H. Sands, Jr. Building<br>303 Research Drive<br>RM 250<br>
Durham, NC 27710<br>P: 919-684-5178<br>*******************************************************<br>
<br><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 6:53 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Tue, Feb 28, 2012 at 3:44 PM, Dialing Pretty <<a href="mailto:hdc123hdc123@yahoo.com">hdc123hdc123@yahoo.com</a>> wrote:<br>
> Will you please give me some suggestion on how to edit the attached file so<br>
> that those electron density not from the protein fragment can be erased? Or<br>
> do you have other methods to produce high quality figure which just shows<br>
> the fragment chain and the fragment eletron density?<br>
<br>
</div>You can use phenix.cut_out_density to do this. �The 'isomesh' command<br>
in PyMOL also offers the ability to only draw mesh within a specified<br>
distance of the selection of interest.<br>
<br>
However, my impression was that this practice is somewhat frowned upon<br>
- it is better to display the actual context of the map instead of<br>
cutting out an idealized portion, which might be more pleasant to look<br>
at but can often be misleading. �The image you attached is already<br>
showing a very clean map that fits the peptides displayed very well; I<br>
don't think it's necessary to clarify it further by reducing the<br>
amount of information it conveys. 泎ut it may just be a matter of<br>
personal taste.<br>
<br>
-Nat<br>
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</blockquote></div><br></div>