[sharp-discuss] analyze data freezes when calculating cross-r's with scaleit
Clemens Vonrhein
vonrhein at globalphasing.com
Wed Nov 18 10:36:09 CET 2009
Hi Francis,
On Tue, Nov 17, 2009 at 02:09:41PM -0700, Francis E Reyes wrote:
> Hi all
>
> I'm doing some bulk analysis of some datasets with AutoSharp and it
> seems to freeze when 'Processing der 2 (reference der 1)'.. This is as
> opposed to processing der 2 with reference to nat.
Seems like scaleit gets stuck - probably in some infinite loop? Can
you check with 'top' if a process 'scaleit' is still running on that
machine and using CPU?
So that looks like a problem in scaleit itself - maybe triggered by
your two derivatives being very different? Or they're both very
incomplete and therefore hardly any overlap between the two
derivatives?
Anything else you could think of?
What happens if you run scaleit by hand with:
scaleit hklin 11-MIR-unique.data.mtz <<e
REFI ANISO
!CONV NCYC 10 ABS 0.001 TOLR 0.00000001
SCAT
EXCL FP SIG 0.0
EXCL FPH1 SIG 0.0
NOWT
LABI FP=FMIDder1 SIGFP=SMIDder1 FPH1=FMIDder2
END
e
or
scaleit hklin 11-MIR-unique.data.mtz <<e
LABI FP=FMIDder1 SIGFP=SMIDder1 FPH1=FMIDder2
END
e
?
Cheers
Clemens
>
> Here's the logfile for the first scaling run (no exclusion)
>
> Thanks!
>
> FR.
>
>
>
>
> SCALEIT
> -------
>
>
> ###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 6.1: SCALEIT version 6.1 : 17/09/08##
> ###############################################################
> User: reyesf Run date: 17/11/2009 Run time: 11:23:32
>
>
> 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.
>
>
>
> Contents
> --------
>
> Command Input
> Input MTZ File
> Output File
> Application of scales and analysis
> -------------------------------------------------------
>
>
> Command Input
> -------------
>
> TITLE
> ANALYSE
> CONVERGE
> LABIN
> EXCLUDE
> GRAPH
> RESOLUTION
> WEIGHT
> NOWT
> REFINE
> SCALE
> SCATTER
> SYMMETRY
> END
> Data line--- TITL autoSHARP(SCALEIT) project MIR
> Data line--- REFI ANISO
> Data line--- CONV NCYC 10 ABS 0.001 TOLR 0.00000001
> Maximum number of cycles 10
> Absolute convergence limit 0.0010
> Tolerance 0.00000
> Data line--- SCAT
> Do Scatter plots of scales
> Data line--- EXCL FP SIG 0.0
> Sigma cutoff, for FP < 0.0 * F excluded
> Data line--- EXCL FPH1 SIG 0.0
> Sigma cutoff, for FPH1 < 0.0 * F excluded
> Data line--- NOWT
> Calculate scales WITHOUT any sigma weighting.
> Data line--- LABI FP=FMIDder1 SIGFP=SMIDder1 FPH1=FMIDder2
> SIGFPH1=SMIDder2 DPH1=DANOder2 SIGDPH1=SANOder2
> FP=
>
> FP= FMIDder1
>
> FP= FMIDder1 FPH= FMIDder2 SMIDder2
>
> Data line--- END
>
>
> Input MTZ File
> --------------
>
>
> OPENED INPUT MTZ FILE
> Logical Name: HKLIN Filename: 11-MIR-unique.data.mtz
>
> * Title:
>
> From Truncate on the 17/11/09
>
> * Base dataset:
>
> 0 HKL_base
> HKL_base
> HKL_base
>
> * Number of Datasets = 5
>
> * Dataset ID, project/crystal/dataset names, cell dimensions,
> wavelength:
>
> 1 unknown
> unknown
> unknown171109:11:15:28
> 97.1340 243.2420 87.4490 90.0000 90.0000 90.0000
> 1.54180
> 2 unknown
> unknownrenamed
> unknown171109:11:15:39
> 96.9150 244.5750 87.8010 90.0000 90.0000 90.0000
> 1.54180
> 3 unknown
> unknownrenamedrenamed
> unknown171109:11:15:52
> 96.2650 242.4190 87.3800 90.0000 90.0000 90.0000
> 1.10490
> 4 unknown
> unknownrenamedrenamedrenamed
> unknown171109:11:16:05
> 95.9020 242.7180 88.1890 90.0000 90.0000 90.0000
> 1.10490
> 5 unknown
> unknownrenamedrenamedrenamedrenamed
> unknown171109:11:16:19
> 96.3210 244.1830 88.0140 90.0000 90.0000 90.0000
> 1.54180
>
> * Number of Columns = 26
>
> * Number of Reflections = 7516
>
> * Missing value set to NaN in input mtz file
>
> * Column Labels :
>
> H K L FMIDnat SMIDnat FreeR_flag FMIDder1 SMIDder1 DANOder1 SANOder1
> ISYMder1 FMIDder2 SMIDder2 DANOder2 SANOder2 ISYMder2 FMIDder3 SMIDder3
> DANOder3 SANOder3 ISYMder3 FMIDder4 SMIDder4 DANOder4 SANOder4 ISYMder4
>
> * Column Types :
>
> H H H F Q I F Q D Q Y F Q D Q Y F Q D Q Y F Q D Q Y
>
> * Associated datasets :
>
> 0 0 0 1 1 1 2 2 2 2 2 3 3 3 3 3 4 4 4 4 4 5 5 5 5 5
>
> * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
>
> 97.1340 243.2420 87.4490 90.0000 90.0000 90.0000
>
> * Resolution Range :
>
> 0.00007 0.05595 ( 122.287 - 4.228 A )
>
> * Sort Order :
>
> 1 2 3 0 0
>
> * Space group = 'C 2 2 2' (number 21)
>
>
> Spacegroup information obtained from library file:
> Logical Name: SYMINFO Filename: /home/reyesf/sharp/database/
> syminfo.lib
>
>
> ****** CENTRIC ZONES ******
>
> CENTRIC Zone 1
> Reflections of type 0kl
>
> CENTRIC Zone 2
> Reflections of type h0l
>
> CENTRIC Zone 3
> Reflections of type hk0
>
>
>
> Output File
> -----------
>
> SPACE GROUP NUMBER 21
> SPACE GROUP NAME C 2 2 2
> POINT GROUP NAME PG222
> NUMBER OF SYMMETRY OPERATORS 8
> NUMBER OF PRIMITIVE SYMMETRY OPERATORS 4
>
>
>
>
>
> ANISOTROPIC DERIVATIVE TO NATIVE SCALING
> ========================================
>
>
>
> Position of Native F 7
> Position of Derivative F 12
> Number of Cycles 10
> Convergence Limit 0.001000
>
>
>
> Derivative has Anomalous Difference to be Scaled
>
>
>
> Derivative: FP= FMIDder1 FPH= FMIDder2 SMIDder2 DANOder2
> SANOder2
> Initial derivative scale factor (for F) = 0.8094 from 3867
> reflections
>
>
>
>
> The anisotropic scale is applied to the derivative F as
> (derivative scale)* exp( - (B11*H**2 + B22*K**2 + B33*L**2 +
> 2*(B12*H*K + B13*H*L + B23*K*L) ) )
>
> CORRELATION MATRIX ELEMENTS > 0.7
>
> CORRELATION MATRIX ELEMENTS > 0.7
> 1 2 -1.0000 1 3 -0.9353 2 3 0.9353 1
> 4 -0.9815 2 4 0.9815 3 4 0.9092
>
> CORRELATION MATRIX ELEMENTS > 0.7
> 1 2 -1.0000 1 3 -0.9688 2 3 0.9688 1
> 4 -0.9880 2 4 0.9880 3 4 0.9523
>
> CORRELATION MATRIX ELEMENTS > 0.7
> 1 2 -1.0000 1 3 -0.9904 2 3 0.9904 1
> 4 -0.9925 2 4 0.9925 3 4 0.9808
>
> CORRELATION MATRIX ELEMENTS > 0.7
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>
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* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
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