[phenixbb] Refinement with partial model - question

Peter Grey petgxray at gmail.com
Fri Apr 2 08:23:36 PDT 2010

Hi Pavel,

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.
Some of these points are described in  "Refinement of severely incomplete
structures with maximum likelihood in *BUSTER-TNT"* E.
P. Roversi<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Roversi,%20P.>,
C. Vonrhein<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Vonrhein,%20C.>,
C. Flensburg<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Flensburg,%20C.>,
S. M. Lea<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Lea,%20S.M.>and
Bricogne (2004)<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Bricogne,%20G.>
* Acta Cryst.* (2004). D*60*, 2210-2221.
As for better ways to calculate masks for severely partial/wrong models:
EM/SAXS models of the entire structure.
When NCS is available, density modification+averaging will yield a mask that
may cover the entire protein.


On Fri, Apr 2, 2010 at 5:00 PM, Ed Pozharski <epozh001 at umaryland.edu> wrote:

> On Thu, 2010-04-01 at 17:06 -0700, Pavel Afonine wrote:
> > I still don't see why it is necessary / important.
> > Also, if you know a better way of mask calculation (or alternative
> > way
> > that sometimes may be better), then I would rather implement that
> > then
> > spend time on an option to allow a user-made mask.
> It may be important to those who would like to experiment with masks but
> don't have time or interest in creating their own crystal structure
> refinement software.
> For instance, long time ago I, like many others before and after, have
> discovered that sometimes there are empty cavities inside proteins,
> which get filled with bulk solvent, resulting in negative density blobs.
> Not a big deal, really, but it was possible to appease the inner
> nitpicker by generating a mask in CNS, running it through USF's MAMA to
> remove isolated islands and supplying it to CNS refinement as an
> external mask.  I haven't seen much change in R-factors (naturally), but
> the negative density was gone.
> Now, I can suggest this as a "better way of mask calculation" (and who
> knows, maybe it's already implemented although I can't find anything
> suggesting it on the website).  Expectation is that you have to be
> convinced that it works at least in some cases.  Catch-22:  suggestions
> will be implemented only if evidence is provided to demonstrate that
> suggested changes in the algorithm have some effect.  Which can't be
> done without implementing the suggestion.
> Ultimately, this question tests what is the philosophy of phenix as the
> software.  Specifically, if software users are encouraged to experiment
> with possible improvements, or such activities are exclusive to
> developer team.
> Cheers,
> Ed.
> --
> Edwin Pozharski, PhD, Assistant Professor
> University of Maryland, Baltimore
> ----------------------------------------------
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
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> When a nation falls to chaos then loyalty and patriotism are born.
> ------------------------------   / Lao Tse /
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