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Out of Memory Errors
by Heather Condurso 21 Apr '11

21 Apr '11

Hello all, I am currently running the Phenix GUI version 1.7-650 on an iMac with an 3.2Ghz Intel Core i3 processor, 8GB of memory operating under OS 10.6. During many of my runs (mostly AutoMR runs but sometimes refine) I get out of memory errors. I have my system booted in 64 bit mode and I watch the activity monitor and find that phenix doesn't use much more than 2GB of memory. My search model is very large. My unit cell contains 4 trimers (each monomer is 48kDa). I hadn't encountered this issue until I began to increase my search model from one trimer to four. Do you have any suggestions as to how I could avoid this error without minimizing my search model? Often my AutoMR runs get the out of memory error at the start of refinement, but just now the memory was exhausted during the fast rotation function. During this run I used all default parameters with a max res of 4.0 and RMSD of 1.0. Any advice you can give would be greatly appreciated! Heather

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R free test set size
by Yuri 20 Apr '11

20 Apr '11

hello everyone, I just noticed that the latest model I am working on has only 2% of reflections marked as free R after refinement! I usually give the GUI the .sca files out of HKL2000 that do not have an Rfree array pre-defined. The GUI lets you know about the lack of it and asks me if I want generate a test set of 10%. I say yes. However the pdb header shows the only 2.14% are chosen for free R. I see that some of my other models (lower resolution) have test arrays of around 7-10% as I would expect. How can I explicitly define the size I want? Thanks -- Yuri Pompeu

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optimizing weights
by Alexandra Deaconescu 20 Apr '11

20 Apr '11

Dear all: I would like to optimize my weights during Phenix refinement. I am running Phenix 1.6.4-486 using the gui, and I have checked the "optimize weights", but I cannot see the results of the optimization in the output, so I do not know the relationship between Rfree/geometry and wc and wxc_scale (I might not want to pick the automatically selected wxc_scale for the lowest Rfree, but would like to find a reasonable values to give me good geometry). Some earlier posts indicated that this is not output in the log file, but I am running a more recent version... Also, in case I wanted to adjust the weights manually, do I have set wxc_scale AND check the fix wc at the same time in the gui? Or just one of them? What would be typical values to start with at 2.8A (even if the answer depends on the particular data)? Same question for the ADP refinement.... I am working at 2.8A and my B factors are high (higher I think than what one would expect at this resolution). Thanks for your help, Alex -- Alexandra M. Deaconescu, Ph.D. Research Associate, HHMI c/o Grigorieff Laboratory Rosenstiel Center MS029 Brandeis University 415 South St. Waltham, MA 02454 phone: 781-736-2498 For FEDEX Brandeis University Kalman Receiving Dock 415 South St. Waltham, MA 02454

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obtaining f'/f'' from solved structures and comparison to a fluorescence scan
by Francis E Reyes 20 Apr '11

20 Apr '11

Hi phenixer's I'm in need of reliable f'/f'' for my heavy atom (that isn't Sasaki tables which I believe is for free, unbound atoms). I've used group_anomalous in phenix.refine before so I'm sure a phenix utility is capable of extracting it. I wanted to if it's possible to extract it from several solved structures (I have the DANO/SIGDANO, F(+)/F(-), or if needed the original I(+)/I(-)) I'm curious to see if there's wide variation and whether it'd be as reliable (or even better) than actually taking a fluorescence scan (and of course use the values for my current phasing challenge as a starting point). F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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AutoSol
by Nora Cronin 18 Apr '11

18 Apr '11

Is have 2 difference anomalous datasets with two different heavy atoms. I can input 2 SAD datasets in AutoSol using the Wavelength and Group = keywords. How do I input 2 different crystal_info keywords since this keyword does not accept the Group= option? cheers Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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unusual maps and Rfree for 1.75 structure
by Yuri 17 Apr '11

17 Apr '11

>>you did not mention the resolution... From your email I guess it is 1.9A, is it correct? It is 1.75A. But like I said the maps right now do not look like those of 1.75 resolution. my 1.9 maps looked way better... The P1 strategy is valid. I will also try processing without the screw axis P 4 2 2, or maybe even P 4 21 2. It looks like the other systematic absences are ok (they are pretty weak reflections). -- Yuri Pompeu

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unusual maps and Rfree for 1.75 structure
by Yuri 16 Apr '11

16 Apr '11

I am solving a structure of an enzyme that I have solved many times before, the only difference is a single mutation in the active site. The crystal grew in basically exact conditions (macroscopically speaking they look different) as the other mutants I had. I scaled the data P 43 21 2 Rsym 0.068. Like all the other data sets I had before. This time however, the initial model has Rfree of about 0.27 and the maps look more like those of a 2.5 - 2.8 structure. My experinence with this enzyme is that I should be looking at around 0.22 or lower Rfree, and pretty clear maps as I saw for my 1.9 structure. Xtriage does not detect any pathologies. I rececked my scaling log file, and it lists the systematic absences for the data. I see some that are not that "weak" for instance : h k l I/sigma 0 0 1 6.0 0 0 2 5.8 0 0 13 7.8 So I am inclined to reprocess my data in P 4 2 2. Are these "symptoms" of a possible wrong space group assignment? Is there something else obvious I am overlooking? Thank you -- Yuri Pompeu

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Re: [phenixbb] Autobuild error -- merging results of nearly-finished OMIT and autobuild runs
by Thomas C. Terwilliger 15 Apr '11

15 Apr '11

Dear Nick, I'm sorry for the error ("[Errno 5] Input/output error") that you are getting with your i7-based PC's with Fedora 14. I have not seen this error before, but we can try to debug it with "debug=true" and also I have a work-around for combining the files that you already have created so you don't need to rerun your whole jobs. Can you possibly run this quick test job to try and get it to fail: phenix.autobuild $PHENIX/phenix_regression/wizards/perfect.mtz \ input_labels="FP SIGFP" \ map_file=$PHENIX/phenix_regression/wizards/perfect.mtz \ input_map_labels="FP PHIC FOM" \ seq_file=$PHENIX/phenix_regression/wizards/seq.dat \ resolution=3.0 \ solvent_fraction=.6 \ model=$PHENIX/phenix_regression/wizards/coords.pdb \ rebuild_in_place=True \ n_cycle_rebuild_min=1 \ n_cycle_rebuild_max=1 \ multiple_models=True \ multiple_models_number=1 \ multiple_models_group_number=2 \ highest_resno=200 \ debug=true This takes about 5 minutes. If it fails, can you send me (terwilliger(a)lanl.gov, not the list) the end out the output where it gives a traceback of where the error occurred? Combining files from a nearly-complete autobuild run with rebuild-in-place=true You can combine models with autobuild, providing all models have exactly the same set of atoms (aside from any solvent) by editing this script (basically you run a dummy autobuild run to create a directory and database entries, then you copy your files there, then you run autobuild and tell it to carry on and do the combine step): -------------------------------------------------------- #!/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 ------------------------------------------------------- Combining OMIT runs that have been run on separate computers or that come from a nearly-completed omit run: You can do this by copying all the individual mtz files with map coefficients for omit regions to a single directory and running a script like this one: (NOTE: you need to ensure that the OMIT regions are defined the same in the runs where you got your overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc files and this run. You ensure that with the n_xyz command that sets the grid. You can copy this from one of your resolve log files created when you ran your omit (i.e., AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0/resolve.log will have a line "nu nv nw: 32 32 32 " and you copy those numbers). ------------------------------------ #!/bin/csh -f # COMBINE OMIT SCRIPT phenix.resolve<<EOD hklin exptl_fobs_phases_freeR_flags.mtz labin FP=FP SIGFP=SIGFP n_xyz 32 32 32 # YOU MUST SET THIS BASED ON THE nu nv nw in a resolve log file. solvent_content 0.85 no_build ha_file NONE combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_2 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_3 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_4 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_5 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_6 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_7 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_8 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_9 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_10 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_11 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_12 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_13 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_14 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_15 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_16 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_17 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_18 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_19 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_20 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_21 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_22 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_23 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_24 omit EOD # END OF COMBINE OMIT SCRIPT All the best, Tom T >> Dear Phenix Developers, >> >> I have been experiencing problems with autobuild whenever I try to rebuild >> an MR model or calculate a composite OMIT map. These tasks always end the >> same way: with "[Errno 5] Input/output error". The failure always happens >> when the run is basically finished and trying to combine the output from >> multiple tasks. My first thought was that my hard drive was full or fixing >> to crash, but these problems happen across several machines and have persisted through multiple official and nightly Phenix releases (currently >> running 1.7-634). The computers that cannot run autobuild successfully are >> both core i7-based PCs running Fedora 14 (though these problems also occurred running earlier Fedora versions). My older xeon-based PC runs autobuild without any trouble, which makes me think this a core i7-related >> problem. I have searched the PhenixBB archive and have not turned up any >> similar problems - have any other users experienced trouble with Phenix and core i7? Is there a work-around I ca >> n use to manually combine the various outputs? The core i7 machines are >> so much faster, I would really like to solve this problem so that I can stop relying on my aging xeon PC for these long calculations. I have included the end of two log files for reference. Also, autosol runs fine >> on the core i7 computers and successfully builds wonderful models from my >> SeMet SAD data. Thank you for Phenix and for any advice you can give. >> >> Best wishes, >> Nick Silvaggi >> >> P.S. I apologize if this message appears twice - I sent it once from an address that was not registered with the BB and decided to re-send from a >> registered address. >> >> Autobuild after MR: >> ----------------------------------------------------------------------------------------------------- Standard build in parallel starting with refine.pdb_1 >> This is the first try at building this model >> Try: 1 building 1 model >> Try: 2 building 1 model >> Try: 3 building 1 model >> Running up to 3 jobs in parallel... with total of 3 jobs >> >> Splitting work into 3 jobs and running with 3 processors using sh background=True in >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0 >> >> Starting job 1...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_3.log Collecting all runs now >> *************ERROR ENDING ******************* >> >> ******************************************************************************** Failed to carry out AutoBuild_build_cycle: >> >> [Errno 5] Input/output error >> ******************************************************************************** >> >> *************ERROR ENDING ******************* >> >> >> Calculating SA composite omit map: >> ----------------------------------------------------------------------------------------------------- Starting job 34...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_34.log Starting job 35...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_35.log Starting job 36...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_36.log Collecting all runs now >> *************ERROR ENDING ******************* >> >> ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: >> >> [Errno 5] Input/output error >> ******************************************************************************** >> >> *************ERROR ENDING ******************* >> >> Nicholas R Silvaggi, Ph.D. >> University of Wisconsin, Milwaukee >> Department of Chemistry and Biochemistry >> 3210 North Cramer St >> Milwaukee, WI 53211 >> >> Office: Chemistry 272B >> Phone: 414-229-2647 >> silvaggi(a)uwm.edu >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Autobuild error
by Nicholas R Silvaggi 15 Apr '11

15 Apr '11

Dear Phenix Developers, I have been experiencing problems with autobuild whenever I try to rebuild an MR model or calculate a composite OMIT map. These tasks always end the same way: with "[Errno 5] Input/output error". The failure always happens when the run is basically finished and trying to combine the output from multiple tasks. My first thought was that my hard drive was full or fixing to crash, but these problems happen across several machines and have persisted through multiple official and nightly Phenix releases (currently running 1.7-634). The computers that cannot run autobuild successfully are both core i7-based PCs running Fedora 14 (though these problems also occurred running earlier Fedora versions). My older xeon-based PC runs autobuild without any trouble, which makes me think this a core i7-related problem. I have searched the PhenixBB archive and have not turned up any similar problems - have any other users experienced trouble with Phenix and core i7? Is there a work-around I can use to manually combine the various outputs? The core i7 machines are so much faster, I would really like to solve this problem so that I can stop relying on my aging xeon PC for these long calculations. I have included the end of two log files for reference. Also, autosol runs fine on the core i7 computers and successfully builds wonderful models from my SeMet SAD data. Thank you for Phenix and for any advice you can give. Best wishes, Nick Silvaggi P.S. I apologize if this message appears twice - I sent it once from an address that was not registered with the BB and decided to re-send from a registered address. Autobuild after MR: ----------------------------------------------------------------------------------------------------- Standard build in parallel starting with refine.pdb_1 This is the first try at building this model Try: 1 building 1 model Try: 2 building 1 model Try: 3 building 1 model Running up to 3 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running with 3 processors using sh background=True in /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0 Starting job 1...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_3.log Collecting all runs now *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: [Errno 5] Input/output error ******************************************************************************** *************ERROR ENDING ******************* Calculating SA composite omit map: ----------------------------------------------------------------------------------------------------- Starting job 34...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_34.log Starting job 35...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_35.log Starting job 36...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_36.log Collecting all runs now *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: [Errno 5] Input/output error ******************************************************************************** *************ERROR ENDING ******************* Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211 Office: Chemistry 272B Phone: 414-229-2647 silvaggi(a)uwm.edu

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parallel structure comparison
by Kendall Nettles 14 Apr '11

14 Apr '11

Dear PHENIX developers, In this weeks build, when I launch coot from the structure comparison results, no models or maps are loaded. It works in the last major release. Also, in the major release version the ligands are stripped out. Is this a bug? If not, I would like to request that the ligands be left in the structures. Thanks so much Kendall

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