[phenixbb] Phaser output and error messages

Ian Stokes-Rees ijstokes at crystal.harvard.edu
Sun Nov 15 05:13:47 PST 2009

I'm having some discussion with a colleague about phaser output (we're 
using Phaser 2.1.4).  We haven't been able to find any documentation 
which can clarify our situation, and I'm hoping someone on the list can 
help answer these questions.  I should mention that I am relatively new 
to Phaser.

1. PHASER.sol files:  Which "SOLU SET" does Phaser consider to be the 
best?  The first or the last?  Or the one with the highest LLG, wherever 
that may be?  In our experience of running Phaser over several MTZ files 
with a range of models the best Phaser solution has always been the 
first, and this has had the highest LLG.

Note: this is with "untuned" Phaser settings for identity, solvent 
fraction, or number of search models in ASU -- our goal is to do a first 
run with "generic" settings for these over a larger set of models, then 
(from TFZ and LLG scores) select a subset for which we will tune Phaser 
parameters and PDB search model variations.

2. If we are right that the first "SOLU SET" entry is indicative of the 
potential for the search model to form a good MR candidate, then is it 
the case that the first entry is the first Phaser solution that is 
computed?  Or is the PHASER.sol file a sorted list output at the end of 
the run?  From my reading of the documentation it is output in order of 
computation, and *for our purposes* (if my first statement in this 
question is correct) Phaser can stop after it outputs this first 
solution.  Is there some way to tell Phaser to stop after the first 
solution is output?

I realize that this doesn't sound like it makes sense (how could Phaser 
know to pick the best solution first, and even if it could, why would it 
ever continue past this point), however I ask because we have put a 10 
minute timeout into our Phaser runs and we have many situations where we 
get a timeout but PHASER.sol has already been generated and the best LLG 
solutions are output first.  It leaves me wondering why it didn't just 
stop on its own after outputting the first result instead of being 
aborted by our (external) timeout that terminates the process?

3. PHASER.sol files: For single domain search models, we usually get 
output of the form:

SOLU SET  RFZ=4.5 TFZ=5.2 PAK=0 LLG=14 LLG=14
SOLU 6DIM ENSE model1 EULER  242.049   45.040  326.088 FRAC -0.09425  
0.50268  0.42575

however we see three variations:

i) No LLG:

SOLU 6DIM ENSE model2 EULER   59.983   69.335  319.701 FRAC -1.17131 
-0.70030  0.23150

ii) One LLG:

SOLU SET  RFZ=3.7 TFZ=4.6 PAK=0 LLG=25
SOLU 6DIM ENSE model3 EULER  293.943  128.068  332.147 FRAC  0.06273  
0.13175  0.25054

iii) Two LLG entries, but with different values:

SOLU SET  RFZ=3.8 TFZ=4.1 PAK=0 LLG=21 LLG=20
SOLU 6DIM ENSE model4 EULER  278.058  129.347   33.292 FRAC  0.28446  
0.29011 -0.07986

4. Occasionally we get an error that we don't understand:

FATAL RUNTIME ERROR: No scattering in pdbfile model1.pdb

What does this mean?  Is there a problem with the PDB file?  We can't 
see anything obvious in the ones which produce this error.



Ian Stokes-Rees, Research Associate
SBGrid, Harvard Medical School

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