[phenixbb] Very very small Phaser Bug
James Fraser
jamesfraser at berkeley.edu
Mon Dec 10 21:05:34 PST 2007
This is a fairly trivial bug, but I thought I'd report it anyway (I'm
not sure whether the problem is with the phenix.automr (rc6 build) or
with all phaser implementations (the one included is: 2.1.1 so I've
emailed both lists):
when running phaser in data that was scaled in P 31 2 1, I used
phenix.automr to automate MR searches in all spacegroups that are
indistinguishable by systematic absences with:
phenix.automr template.pdb final_P3121.sca RMS=1 mass=17000
rebuild_after_mr=False copies=1 use_all_plausible_sg=True
The program correctly finds the solution in P3221 with a log
likelihood gain of 1000 vs 20 for P3121, everything is fine in the
outputted PDB CRYST1 line and MTZ; however the log file annoyingly
mentions the spacegroup for the last time with "Final space group:P 31
2 1" even though elsewhere in the log file it correctly lists
"SpaceGroup of Solution: P 32 2 1". I've excerpted the log file
below. If this is the intended behaviour and not a bug, then I
apologize but find it quite counterintuitive.
Just a small bug, haven't seen if this behaviour occurs in other
systematic absence-equivalent space groups.
Best,
jf
**BEGIN LOG
SpaceGroup of Solution: P 32 2 1
SINGLE solution
Solution written to PDB file: /Users/jfraser/data/AutoMR_run_7_/MR.1.pd
b
Solution written to MTZ file: /Users/jfraser/data/AutoMR_run_7_/MR.1.mt
z
Solution log-likelihood gain: 1056.73
Solution annotation (history): RFZ=11.9 TFZ=27.5 PAK=0 LLG=850 LLG=1057
AUTOMR RUN: 7
Files in directory : AutoMR_run_7_
CRITERIA FOR PHASER MR RUN:
selection_criteria_rot : Percent_of_best
selection_criteria_rot_value : 75
use_all_plausible_sg : Yes
overlap_allowed :
List of space groups tested:
['P 3 2 1', 'P 31 2 1', 'P 32 2 1']
Final space group:P 31 2 1
CURRENT ENSEMBLES:
ENSEMBLE ID: ensemble_1
FILE: template.pdb RMS = 1.0
ENSEMBLES USED IN SEARCH: ensemble_1
**************** SOLUTION MR *******
Log likelihood gain for solution MR: 1056.7344
Output PDB files for solution MR: MR.1.pdb
Output MTZ files for solution MR: MR.1.mtz
**END LOG
--
James Fraser
jamesfraser at berkeley.edu
Alber Lab
356 Stanley Hall, QB3
UC Berkeley
Berkeley, CA 94720
http://ucxray.berkeley.edu/~jfraser/
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