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Re: [phenixbb] reduce hangs
by Andreas Förster 05 Dec '13

05 Dec '13

Dear all, I'm not sure how much of my conversation with Jeff Headd and the comments from others that I received made it onto the mailing list. The problem with reduce being stuck in an infinite loop and refinement never completing has now a workaround, if no solution: Mark van Raaij pointed out that running refinement repeatedly while varying the number of cores would eventually avoid the infinite loop. I didn't observe that, but while running refinement with a handful of Xeons got stuck, running the same job with the same executable on the same OS with a bucketful of Opterons instead succeeded. As I said, there's no solution but a number of ways to get unstuck if you find yourself in the same situation like Mark and me. Best. Andreas -------- Original Message -------- Subject: Re: [phenixbb] reduce hangs Date: Wed, 4 Dec 2013 09:46:20 -0500 From: Jeff Headd <jjheadd(a)lbl.gov> To: Andreas Förster <docandreas(a)gmail.com> If the different machine is a slightly different architecture it's possible that it may run, even under the same OS version. My guess is that it's down to slight floating point differences in the coordinates throughout the course of refinement, but it's so hard to pinpoint. If you have access to other machines it is probably worth trying. <snip> Jeff

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Coot not allowing real space refinement when connected to phenix
by Jobichen Chacko 05 Dec '13

05 Dec '13

Dear All, I recently upgraded to latest version of coot (version0.7.2). When I try to do the Real space refine zone option, coot is giving the following complaint (Refinement setup failure. Failed to find restraints for PROLYSILE). But it works fine when I open coot separately from a terminal and read the pdb and mtz file. I downloaded this coot along with the ccp4 package and it also works fine when I open from ccp4 interface. Any suggestions will be much appreciated. Jobi

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hi.
by Hexi Zhang 04 Dec '13

04 Dec '13

http://satis.egitmeni.org/dxibo/axzjmylquusc.html Hexi Zhang

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reduce hangs
by Andreas Förster 04 Dec '13

04 Dec '13

Dear all, I'm refining a structure with 11 molecules in the asymmetric unit. Recently I took out NCS (data are to 2.2A and differences between molecules of interest). Refinement now stalls halfway through with two reduce jobs running at 100% CPU. The current job has been sitting like this for four days. The last entry in the log file are a few XYZ individual lines. Refinement includes XYZ, TLS, individual B, weight optimization. I launched 8 cycles. Phenix hangs after 4_bss. I've observed this twice in a row. Any suggestions to overcome this, short of going back to using NCS? This is with Phenix dev-1538 on RHEL 6.3. Thanks. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London

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AutoSol/Heavy atom sites/outside the model
by Egor Tchesnokov 04 Dec '13

04 Dec '13

Thank you for the feedback. WinCoot 0.7/Draw/Cell Symmetry brings up "Show Symmetry" window, which only allows to alter the display but not to coincide the heavy atom sites with the model. Am I not looking at the right menu in Coot ? Thank you for your time and help. Egor

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Autobuild combine
by Heather L Condurso 03 Dec '13

03 Dec '13

Hi all, I am still having issues with Autobuild giving errors during the combine step. I've downloaded the latest build and hope that will solve the problem, but in the mean time I'm having an issue trying to combine the models. I've been following the script: #!/bin/csh -f #COMBINE_MODELS SCRIPT if (-d PDS || -d AutoBuild_run_1_) then echo "Please run in a directory without PDS or AutoBuild_run_1_" exit 1 endif echo "Setting up combine models with a dummy run. NOTE: multiple_models_group_number must be correct" phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat combine_only=true multiple_models_group_number=2 multiple_models_number=1 > dummy_autobuild.log echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS" mkdir AutoBuild_run_1_/MULTIPLE_MODELS cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp map_coeffs_1.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1 cp map_coeffs_2.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2 ls AutoBuild_run_1_/MULTIPLE_MODELS/ echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS" phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 > autobuild_combine.log # END OF COMBINE_MODELS SCRIPT # Here are the two log files. I used the expl_fobs_phases_freeR_flags.mtz as fobs.mtz and changed each overall_best.pdb and overall_best_refine_map_coeffs.mtz as the model and map to combine. Thanks, Heather

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AutoSol/Heavy atom sites/outside the model
by Egor Tchesnokov 03 Dec '13

03 Dec '13

Hello, Level: beginner 1. Data collected at wavelength of 0.9537 2. Ran Xtriage: anomalous data seem to extend to 2.2 A 3. Ran Phaser-MR to get partial model (1 copy in AU) 4. Ran AutoSol using partial model and anomalous data AutoSol finds heavy atom sites (FOM=0.69; Overall score=75.6+/-3.3). Coot displays model/density without heavy atoms Heavy atoms are displayed outside the model (using zoom out). Question: what did I do wrong? Thank you for your time and help. Egor

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Red patches of electron density
by Singh, Bishal 02 Dec '13

02 Dec '13

Hi, I am solving a crystal structure at 1.2 Å with completeness 97.3% in the highest resolution shell. There are few small patches of red electron densities on the main chain of a flexible loop at a contour level of ~3sigma of difference ED map. Refinement parameters were following: XYZ coordinates, individual B-factor, optimize X-ray/stereochemistry weight, optimize X-ray/ADP weight and individual Anisotropic ADP for amino acids excluding hydrogen. Target weights are as default in phenix.refine. I already have observed two alternative conformation for this region in another crystal structure. Therefore I am thinking that these red patches are because of lower occupancy of these residues. Please suggest me what shall I do. I shall be grateful for your words. With regards, Bishal Singh University of Heidelberg, Germany

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Iterative build omit map error
by Heather L Condurso 28 Nov '13

28 Nov '13

SO just as my omit map run should have finished, it gave an error instead. I'm running 1.8.4-1496 on a Mac with OSX 10.6.8 and 8GB of memory. Here is the end of the log file: Splitting work into 32 jobs and running with 1 processors using sh background=False in /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_3.log Starting job 4...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_4.log Starting job 5...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_5.log Starting job 6...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_6.log Starting job 7...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_7.log Starting job 8...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_8.log Starting job 9...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_9.log Starting job 10...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_10.log Starting job 11...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_11.log Starting job 12...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_12.log Starting job 13...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_13.log Starting job 14...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_14.log Starting job 15...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_15.log Starting job 16...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_16.log Starting job 17...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_17.log Starting job 18...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_18.log Starting job 19...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_19.log Starting job 20...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_20.log Starting job 21...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_21.log Starting job 22...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_22.log Starting job 23...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_23.log Starting job 24...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_24.log Starting job 25...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_25.log Starting job 26...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_26.log Starting job 27...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_27.log Starting job 28...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_28.log Starting job 29...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_29.log Starting job 30...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_30.log Starting job 31...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_31.log Starting job 32...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log : /TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz Rebuilding side chains from Build_composite_refined_3.pdb Refining model: edit_model.pdb approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.0197876048373 approx_equal ERROR 0.0197856373852 approx_equal ERROR Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log : /TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz Rebuilding side chains from Build_composite_refined_3.pdb Refining model: edit_model.pdb approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.0197876048373 approx_equal ERROR 0.0197856373852 approx_equal ERROR Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz ******************************************************************************** Can this be salvaged? It took 5 days to run. I found a section about this in the documentation, but I can't find the maps for each region overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. I can only find working_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. Will these maps work? Can you tell what the error means so that I can avoid this problem in the future? Thanks, Heather

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zero B-factors
by Edna Patricia Matta, Ms 26 Nov '13

26 Nov '13

Hello, Recently I did submit a structure to the PDB but they found that some atoms had zero value for the B-factors. I am new in this filed and I do not know what to do. There have been reports of problems with some versions of phenix about this. I used Phenix 1.8. I repeted the refinement doing restrain NCS-related B-factors but I do not find where to check for the the B-factor values in the the log file. Somebody can help me? Thanks a lot, Edna

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