[phenixbb] Refinement with partial model - question

Ed Pozharski epozh001 at umaryland.edu
Fri Apr 2 08:00:17 PDT 2010

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.



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.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

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