Pointless should supercede sortmtz, at least for most purposes, but I agree it should be increased
Actually it's inconsistent in the source code, elsewhere there is PARAMETER (NMAX_MEM = 16000000) but that may not matter Phil On 18 Nov 2011, at 15:50, Jacob Keller wrote: > Okay, it seems there is utility to Pointless--problem solved! Maybe > developers should consider upping the limit, though? > > Thanks very much, > > Jacob > > On Fri, Nov 18, 2011 at 9:45 AM, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: >> There's a limit set in CCP4/lib/src/sorting_main.f >> >> C NMAX_MEM increased from 16000000 to 32000000 >> PARAMETER (NMAX_MEM = 32000000) >> >> which you could change and recompile (:-)) >> >> You can combine unmerged files in Pointless, which is usually the best >> method, but that reads everything into memory so you may well hit system >> limits unless you have a 64-bit system with lots of memory (and a 64-bit >> build) >> >> Phil >> >> >> >> On 18 Nov 2011, at 15:36, Jacob Keller wrote: >> >>> Dear Crystallographers, >>> >>> I am getting an error when I try to merge two mtz's from mosflm, one >>> with 180 and one with 360 frames, each from different but similar >>> crystals--see below. I can't imagine this really exceeds the max >>> number of records, so what am I doing wrong? Additionally but related, >>> what is the optimal procedure in CCP4 for combining data from two >>> similar crystals? >>> >>> JPK >>> >>> >>> >>> #CCP4I VERSION CCP4Interface 2.1.0 >>> #CCP4I SCRIPT LOG sortmtz >>> #CCP4I DATE 18 Nov 2011 09:26:28 >>> #CCP4I USER 'UNKNOWN' >>> #CCP4I PROJECT NatVSulP >>> #CCP4I JOB_ID 26 >>> #CCP4I SCRATCH C:/Ccp4Temp >>> #CCP4I HOSTNAME chloe >>> #CCP4I PID 5396 >>> >>> <html> <!-- CCP4 HTML LOGFILE --> >>> <hr> >>> >>> <a name="smsortmtz"><h2>SORTMTZ</h2></a> >>> <pre> >>> >>> ############################################################### >>> ############################################################### >>> ############################################################### >>> ### CCP4 6.2: SORTMTZ version 6.2 : 06/09/05## >>> ############################################################### >>> User: Jacob Run date: 18/11/2011 Run time: 09:26:28 >>> >>> >>> Please reference: Collaborative Computational Project, Number 4. 1994. >>> "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. >>> D50, 760-763. >>> as well as any specific reference in the program write-up. >>> >>> </pre> >>> >>> <a name="tocSORTMTZ"><h2>Contents</h2></a> >>> <ul> >>> <li><a href="#commandSORTMTZ">Command Input</a> >>> <li><a href="#inputSORTMTZ">Input File Details</a> >>> <li><a href="#outputSORTMTZ">Output File Details</a> >>> <li><a href="#outSORTMTZ">Header Information for Output MTZ File</a> >>> </ul> >>> <hr> >>> >>> <a name="commandSORTMTZ"><h3>Command Input</h3></a> >>> <a >>> href="C:\CCP4-Packages\ccp4-6.2.0\html/sortmtz.html#ascend">ASCEND/DESCEND</a> >>> <a href="C:\CCP4-Packages\ccp4-6.2.0\html/sortmtz.html#sort_keys">SORT >>> KEYS</a> >>> <pre> >>> Data line--- ASCEND >>> Data line--- H K L M/ISYM BATCH >>> Data line--- >>> "C:/Users/Jacob/Desktop/Dallos_Lab/Analysis/NatVSulP/lo_res_natvsulp_jpk_raw.mtz" >>> </pre> >>> <hr> >>> >>> <a name="inputSORTMTZ"><h3>Input File Details</h3></a> >>> <pre> >>> >>> OPENED INPUT MTZ FILE >>> Logical Name: >>> C:/Users/Jacob/Desktop/Dallos_Lab/Analysis/NatVSulP/lo_res_natvsulp_jpk_raw.mtz >>> Filename: >>> C:/Users/Jacob/Desktop/Dallos_Lab/Analysis/NatVSulP/lo_res_natvsulp_jpk_raw.mtz >>> >>> * Title: >>> >>> Untitled >>> >>> * Base dataset: >>> >>> 0 HKL_base >>> HKL_base >>> HKL_base >>> >>> * Number of Datasets = 1 >>> >>> * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: >>> >>> 1 New >>> New >>> New >>> 82.0600 82.0600 159.2500 90.0000 90.0000 90.0000 >>> 0.97856 >>> >>> * Number of Columns = 18 >>> >>> * Number of Reflections = 1526614 >>> >>> * Missing value set to NaN in input mtz file >>> >>> * Number of Batches = 360 >>> >>> * Column Labels : >>> >>> H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH >>> LP MPART FLAG BGPKRATIOS >>> >>> * Column Types : >>> >>> H H H Y B J Q J Q R R R R R R I I R >>> >>> * Associated datasets : >>> >>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>> >>> * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) >>> >>> 82.0600 82.0600 159.2500 90.0000 90.0000 90.0000 >>> >>> * Resolution Range : >>> >>> 0.00030 0.15998 ( 58.026 - 2.500 A ) >>> >>> * Sort Order : >>> >>> 0 0 0 0 0 >>> >>> * Space group = 'P43212' (number 96) >>> >>> >>> Spacegroup information obtained from library file: >>> Logical Name: SYMINFO Filename: >>> C:\CCP4-Packages\ccp4-6.2.0\lib\data\syminfo.lib >>> >>> 5 sort keys, in columns 1 2 3 4 5 >>> </pre> >>> <hr> >>> >>> <a name="outputSORTMTZ"><h3>Output File Details</h3></a> >>> <pre> >>> 1526614 records read from file 1 >>> Data line--- >>> "C:/Users/Jacob/Desktop/Dallos_Lab/Analysis/NatVSulP/lo_res_natvsulp_chs_raw_batched_up_to_401.mtz" >>> </pre> >>> <hr> >>> >>> <a name="inputSORTMTZ"><h3>Input File Details</h3></a> >>> <pre> >>> >>> OPENED INPUT MTZ FILE >>> Logical Name: >>> C:/Users/Jacob/Desktop/Dallos_Lab/Analysis/NatVSulP/lo_res_natvsulp_chs_raw_batched_up_to_401.mtz >>> Filename: >>> C:/Users/Jacob/Desktop/Dallos_Lab/Analysis/NatVSulP/lo_res_natvsulp_chs_raw_batched_up_to_401.mtz >>> >>> * Title: >>> >>> [No title given] >>> >>> * Base dataset: >>> >>> 0 HKL_base >>> HKL_base >>> HKL_base >>> >>> * Number of Datasets = 1 >>> >>> * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: >>> >>> 1 New >>> New >>> New >>> 82.3400 82.3400 161.4500 90.0000 90.0000 90.0000 >>> 0.97940 >>> >>> * Number of Columns = 18 >>> >>> * Number of Reflections = 536433 >>> >>> * Missing value set to NaN in input mtz file >>> >>> * Number of Batches = 180 >>> >>> * Column Labels : >>> >>> H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH >>> LP MPART FLAG BGPKRATIOS >>> >>> * Column Types : >>> >>> H H H Y B J Q J Q R R R R R R I I R >>> >>> * Associated datasets : >>> >>> 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >>> >>> * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) >>> >>> 82.3400 82.3400 161.4500 90.0000 90.0000 90.0000 >>> >>> * Resolution Range : >>> >>> 0.00015 0.16000 ( 82.340 - 2.500 A ) >>> >>> * Sort Order : >>> >>> 1 2 3 4 5 >>> >>> * Space group = 'P43212' (number 96) >>> >>> Too many records >>> SORTMTZ failed to release record to sort procedure, status = 1 >>> >>> SORTMTZ: Sorting failed >>> Times: User: 0.0s System: 0.0s Elapsed: 0:05 >>> </pre> >>> </html> >>> *************************************************************************** >>> * Information from CCP4Interface script >>> *************************************************************************** >>> The program run with command: sortmtz HKLOUT >>> "C:/Users/Jacob/Desktop/Dallos_Lab/Analysis/NatVSulP/lo_res_natvsulp_comb_raw.mtz" >>> has failed with error message >>> SORTMTZ: Sorting failed >>> *************************************************************************** >>> >>> >>> #CCP4I TERMINATION STATUS 0 " SORTMTZ: Sorting failed" >>> #CCP4I TERMINATION TIME 18 Nov 2011 09:26:33 >>> #CCP4I MESSAGE Task failed >>> >>> >>> >>> -- >>> ******************************************* >>> Jacob Pearson Keller >>> Northwestern University >>> Medical Scientist Training Program >>> email: j-kell...@northwestern.edu >>> ******************************************* >> > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-kell...@northwestern.edu > *******************************************