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 <[log in to unmask]> 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: [log in to unmask]
>> *******************************************
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
*******************************************
|