Re: [phenixbb] Problem using MOSFLM-integrated MAD data
Dear All, Thanks to all those who have responded to my previous query. The problem was due to I used MOSFLM raw data without scaling or sorting. I put the MOSFLM data through SORTMTZ and SCALA and output as "unmerged intensities in SCALEPACK format" and that error I mentioned earlier in the BB has gone. SOLVE completed successfully with some possible solutions. But now I have another problem. When RESOLVE tries to run DM, it reported another problem which seems to indicate it cannot read the scala-produced file correctly. The last bit of the log file before AutoSol stopped is as follows. I also print out the first few lines of the scala-produced SCALEPACK-format data file at the bottom for your diagnosis. Can you advise me what went wrong (and how to fix it)? Thanks a lot. Regards. Wai ##################### AutoSol_build AutoSol Run 22 Mon Dec 7 17:07:41 2009 SOLUTION FOR MODEL-BUILDING: Solution 2 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca and taking inverse. Dataset #1 SG="P 21 21 21" SOLUTION FOR MODEL-BUILDING: Solution 1 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca. Dataset #1 SG="P 21 21 21" DM SOLUTION USED FOR MODEL-BUILDING 1:Solution 2 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca and taking inverse. Dataset #1 SG="P 21 21 21" WARNING: As the experimental data have been corrected for anisotropy and no input_refinement_file is available, no refinement will be carried out. Model-building will continue without refinement. Trying to guess refinement file for later use from ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl'] Choosing guess of refinement file for later use from all files: ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl'] FILE TYPE scalepack_no_merge_original_index GUESS FILE TYPE MERGE TYPE sca unmerged TARGET LABELS ['I', 'SIGI'] CONTENTS: ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl', 'sca', 'unmerged', 'P 2 2 2', None, None, ['I', 'SIGI']] File /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl ******************************************************************************** Failed to carry out AutoSol_build: float argument required, not NoneType ******************************************************************************** ########################### SeM8/phnx> more sem8_peak.hkl 4 P222 1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 -1 0 0 0 0 -1 -2 0 1 2 2 0 0 1 608.6 133.4 0 -1 -2 0 1 2 179 0 0 1 660.0 138.4 0 1 -2 0 1 2 176 0 0 2 519.0 130.9 0 -1 -3 0 1 3 4 0 0 1 1409.6 239.7 0 -1 -3 0 1 3 179 0 0 1 1525.0 251.0 -- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
Hi Wai, I'm sorry, that error you have is because I changed some printouts that don't happen very often and I missed a couple cases where there could be either a floating point number or a "None". Could you possibly re-run with "debug=True" and send me the output (which will have a line number where I need to fix the printout)? Or if you prefer just to send me the file (not to the list) I'll run it here and fix the error. All the best, Tom T
Dear All,
Thanks to all those who have responded to my previous query.
The problem was due to I used MOSFLM raw data without scaling or sorting. I put the MOSFLM data through SORTMTZ and SCALA and output as "unmerged intensities in SCALEPACK format" and that error I mentioned earlier in the BB has gone. SOLVE completed successfully with some possible solutions. But now I have another problem. When RESOLVE tries to run DM, it reported another problem which seems to indicate it cannot read the scala-produced file correctly. The last bit of the log file before AutoSol stopped is as follows. I also print out the first few lines of the scala-produced SCALEPACK-format data file at the bottom for your diagnosis. Can you advise me what went wrong (and how to fix it)?
Thanks a lot. Regards.
Wai
#####################
AutoSol_build AutoSol Run 22 Mon Dec 7 17:07:41 2009
SOLUTION FOR MODEL-BUILDING: Solution 2 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca and taking inverse. Dataset #1 SG="P 21 21 21" SOLUTION FOR MODEL-BUILDING: Solution 1 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca. Dataset #1 SG="P 21 21 21" DM SOLUTION USED FOR MODEL-BUILDING 1:Solution 2 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca and taking inverse. Dataset #1 SG="P 21 21 21" WARNING: As the experimental data have been corrected for anisotropy and no input_refinement_file is available, no refinement will be carried out. Model-building will continue without refinement.
Trying to guess refinement file for later use from ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl'] Choosing guess of refinement file for later use from all files: ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl'] FILE TYPE scalepack_no_merge_original_index GUESS FILE TYPE MERGE TYPE sca unmerged TARGET LABELS ['I', 'SIGI'] CONTENTS: ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl', 'sca', 'unmerged', 'P 2 2 2', None, None, ['I', 'SIGI']] File /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl ******************************************************************************** Failed to carry out AutoSol_build:
float argument required, not NoneType ********************************************************************************
###########################
SeM8/phnx> more sem8_peak.hkl 4 P222 1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 -1 0 0 0 0 -1 -2 0 1 2 2 0 0 1 608.6 133.4 0 -1 -2 0 1 2 179 0 0 1 660.0 138.4 0 1 -2 0 1 2 176 0 0 2 519.0 130.9 0 -1 -3 0 1 3 4 0 0 1 1409.6 239.7 0 -1 -3 0 1 3 179 0 0 1 1525.0 251.0
-- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
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participants (2)
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Chen, Yu Wai -
Thomas C. Terwilliger