[phenixbb] Very very small Phaser Bug

Tom Terwilliger terwilliger at lanl.gov
Tue Dec 11 08:28:25 PST 2007

Hi James,
Yes this sounds like a bug to me. I think it is a mis-communication 
between the automr wizard and phaser. We'll check it out.
Thank you!
-Tom T

At 10:05 PM 12/10/2007, you wrote:
>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.
>    SpaceGroup of Solution:  P 32 2 1
>    SINGLE solution
>    Solution written to PDB file:  /Users/jfraser/data/AutoMR_run_7_/MR.1.pd
>    Solution written to MTZ file:  /Users/jfraser/data/AutoMR_run_7_/MR.1.mt
>    Solution log-likelihood gain:  1056.73
>    Solution annotation (history):  RFZ=11.9 TFZ=27.5 PAK=0 LLG=850 LLG=1057
>Files in directory : AutoMR_run_7_
>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
>ENSEMBLE ID: ensemble_1
>FILE: template.pdb  RMS = 1.0
>**************** 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
>James Fraser
>jamesfraser at berkeley.edu
>Alber Lab
>356 Stanley Hall, QB3
>UC Berkeley
>Berkeley, CA 94720
>phenixbb mailing list
>phenixbb at phenix-online.org

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web 
site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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