From: Jacob Keller
Date: 18 November 2011 15:36
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
*******************************************
----------
From: Phil Evans
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
----------
From: Jacob Keller
Okay, it seems there is utility to Pointless--problem solved! Maybe
developers should consider upping the limit, though?
Thanks very much,
Jacob
----------
From: Phil Evans
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
Date: 18 November 2011 15:36
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
*******************************************
----------
From: Phil Evans
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
----------
From: Jacob Keller
Okay, it seems there is utility to Pointless--problem solved! Maybe
developers should consider upping the limit, though?
Thanks very much,
Jacob
----------
From: Phil Evans
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
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