[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 SET RFZ=3.1 TFZ=5.0 PAK=0
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.
Thanks,
Ian
--
Ian Stokes-Rees, Research Associate
SBGrid, Harvard Medical School
http://sbgrid.org
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