[phenixbb] Phaser output and error messages

Ian Stokes-Rees ijstokes at crystal.harvard.edu
Tue Nov 17 09:50:04 PST 2009

Thank you for the quick response.

Randy Read wrote:
> On the point of "tuning" parameters, I'm not sure what you mean.  In a  
> particular case, you should know what you put into your  

This is probably a good point at which to mention that I am not a 
crystallographer or structural biologist, but a computational scientist 
working on parameter sweep mechanisms to tune the molecular replacement 
phase of structure discovery.

I have spoken with structural biologists working in industry who say 
they do exactly kind of parameter tuning and parameter sweep -- rather 
than assume they know more about their crystal/structure properties than 
they think.  I also find in literature "hints" such as Figure 3 in this 
December 2007 Acta D paper on MR (using CCP4 Molrep, not Phaser):


that suggest the underlying algorithms do not rely on parameter settings 
matching "reality" to produce the most promising results -- note in 
Figure 3 a 0.2 and 0.9 completeness give a similar Rfree result.  Of 
course, a priori structure/crystal knowledge would probably allow 
correct selection from the various peaks, but it is still relevant that 
the underlying algorithms in molrep produce similar strong results with 
dramatically different input parameters.

> 2. Given that the potential solutions in the .sol file are sorted by  
> LLG, I'm not sure where the idea would come from that they could be  
> given in the order they were found.  You can follow the solutions in

What confused me here was that the same file is being repeatedly 
over-written as Phaser progresses.

> 4. If Phaser reports that there is no scattering in a model, it means  
> that you have supplied an empty PDB file, or one where all the  

It turns out this was a bug on our part -- In a small number of cases 
(about 2%) our PDB trimming algorithm was inserting bogus END entries 
into the intermediate PDB file.  Phaser (rightly) stopped processing 
when it encountered these, and produced the given error.  Other tools in 
our processing chain were more forgiving, so it appeared to be a Phaser 


Ian Stokes-Rees                            W: http://sbgrid.org
ijstokes at crystal.harvard.edu               T: +1 617 432-5608 x75
SBGrid, Harvard Medical School             F: +1 617 432-5600

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