Hi Pavel,<br><br>Refinement of severely partial models can be greatly facilitated by some way of describing the missing parts or at least knowing were there is solvent and where protein. <br>Some of these points are described in "Refinement of severely incomplete structures with maximum likelihood
in <span class="it"><i>BUSTER-TNT"</i></span><a href="http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Blanc,%20E."> E.
Blanc</a>, <a href="http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Roversi,%20P.">P.
Roversi</a>, <a href="http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Vonrhein,%20C.">C.
Vonrhein</a>, <a href="http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Flensburg,%20C.">C.
Flensburg</a>, <a href="http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Lea,%20S.M.">S.
M. Lea</a> and <a href="http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Bricogne,%20G.">G.
Bricogne (2004)</a><i> Acta Cryst.</i> (2004). D<b>60</b>,
2210-2221.<br>As for better ways to calculate masks for severely partial/wrong models:<br>EM/SAXS models of the entire structure.<br>When NCS is available, density modification+averaging will yield a mask that may cover the entire protein.<br>
<br>Peter.<br><br><br><div class="gmail_quote">On Fri, Apr 2, 2010 at 5:00 PM, Ed Pozharski <span dir="ltr"><<a href="mailto:epozh001@umaryland.edu">epozh001@umaryland.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On Thu, 2010-04-01 at 17:06 -0700, Pavel Afonine wrote:<br>
> I still don't see why it is necessary / important.<br>
> Also, if you know a better way of mask calculation (or alternative<br>
> way<br>
> that sometimes may be better), then I would rather implement that<br>
> then<br>
> spend time on an option to allow a user-made mask.<br>
<br>
</div>It may be important to those who would like to experiment with masks but<br>
don't have time or interest in creating their own crystal structure<br>
refinement software.<br>
<br>
For instance, long time ago I, like many others before and after, have<br>
discovered that sometimes there are empty cavities inside proteins,<br>
which get filled with bulk solvent, resulting in negative density blobs.<br>
Not a big deal, really, but it was possible to appease the inner<br>
nitpicker by generating a mask in CNS, running it through USF's MAMA to<br>
remove isolated islands and supplying it to CNS refinement as an<br>
external mask. I haven't seen much change in R-factors (naturally), but<br>
the negative density was gone.<br>
<br>
Now, I can suggest this as a "better way of mask calculation" (and who<br>
knows, maybe it's already implemented although I can't find anything<br>
suggesting it on the website). Expectation is that you have to be<br>
convinced that it works at least in some cases. Catch-22: suggestions<br>
will be implemented only if evidence is provided to demonstrate that<br>
suggested changes in the algorithm have some effect. Which can't be<br>
done without implementing the suggestion.<br>
<br>
Ultimately, this question tests what is the philosophy of phenix as the<br>
software. Specifically, if software users are encouraged to experiment<br>
with possible improvements, or such activities are exclusive to<br>
developer team.<br>
<br>
Cheers,<br>
<br>
Ed.<br>
<br>
--<br>
Edwin Pozharski, PhD, Assistant Professor<br>
University of Maryland, Baltimore<br>
----------------------------------------------<br>
When the Way is forgotten duty and justice appear;<br>
Then knowledge and wisdom are born along with hypocrisy.<br>
When harmonious relationships dissolve then respect and devotion arise;<br>
When a nation falls to chaos then loyalty and patriotism are born.<br>
------------------------------ / Lao Tse /<br>
<div><div></div><div class="h5"><br>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Peter<br>