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
> *******************************************
