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.
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 [email protected] Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/ _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] 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