[phenixbb] Refinement with partial model - question

Pavel Afonine PAfonine at lbl.gov
Fri Apr 2 08:25:00 PDT 2010

Hi Ed,

> 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 that long ago this problem was brought up by Dirk and Morten, and a 
few more people.

> 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.

Yes, it's another item in the list of things to do. It just has lower 
priority and so will not appear tomorrow.

> 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.

It's for a broad range of users: from experimenters (this is why 
phenix.refine has more than 300 parameters available to play with), to 
newbies that can just run "phenix.refine model.pdb data.mtz".

Plus, if you have some knowledge of Python and crystallography methods, 
you can write your own refinement program using cctbx and mmtbx 
librarier - just use them as Lego constructor. And don't forget to 
experiment along the way.

We have our own endless list of interesting things to implement/try out, 
plus we get great ideas from the user community. If we spend our 
developer's time on doing them all and now, we will never get anywhere. 
So we have to be selective and work only on those that are the most 
important. What's "important" is defined by the amount of user requests 
or by our own considerations.


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