pointless error-summary

From: Rajesh kumar
Date: 19 November 2011 09:49

Thanks to Harry Powell, Phil Evans, De-Feng Li for suggestions and special thanks to Charles Ballard looking in to my data.

The summary is 

Harry Powell and Phil Evans-Pointless  needs update as newer version is up to version 1.6.8 -  the latest copy is at ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.6.8.linux

De-Feng Li- In the log file, Number of batches (1) show that the dataset used in Pointless have been scaled. In fact, the input dataset should be not scaled. You can try it again.

Charles Ballard-I can reproduce the failure using pointless 1.4.10 (ccp4 6.1.13).  It, however, runs successfully with pointless 1.5.22 (ccp4-6.2.0). 1.4.10 is throwing a lot of memory errors, so it is probably a memory problem. I would suggest using a more up-to-date pointless.  You can get that either from CCP4, or just pointless itself from 

ftp://mrc-lmb.cam.ac.uk/pub/pre. 

ps - you will probably get more from the unmerged data

Thanks

Rajesh

Dear all,

mtzdump shows my space group as 'C 2 2 21' (number     20)
pointless gives error "Space group is not in library". part of the log file is following.

I appreciate all the help.

Thanks
Raj


        ******************************************************
        *                                                    *
        *                     POINTLESS                      *
        *                       1.4.5                        *
        *                                                    *
        *   Determine Laue group from unmerged intensities   *
        *     Phil Evans MRC LMB, Cambridge                  *
        * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
        *                                                    *
        ******************************************************

Maximum resolution in file output_7-21.mtz:    2.740
Columns for I, sigI: IMEAN  SIGIMEAN

 Spacegroup information obtained from library file:
 Logical Name: SYMINFO   Filename: /opt/programs/ccp4/ccp4-6.1.13/lib/data/syminfo.lib


===============================================================

>*> Summary of test data read in:
   Resolution range accepted:    47.92        2.74

   Number of reflections  =         18008
   Number of observations =         18008
   Number of parts        =         18008
   Number of batches      =             1
   Number of datasets     =             1
      Project:                   Crystal: unknown          Dataset: unknown210711:15:24:58
         Run number:   1 consists of batches      1 to      1
   Average unit cell:  110.66   112.08   120.78    90.00    90.00    90.00 

Unit cell (from HKLIN file) used to derive lattice symmetry with tolerance   2.0 degrees
 110.66 112.08 120.78  90.00  90.00  90.00

Tolerance (and delta) is the maximum deviation from the
 expected angle between two-fold axes in the lattice group

Lattice point group: P 4 2 2
Reindexing or changing symmetry
Reindex operator from input cell to lattice cell: [-1/2h-1/2k,-1/2h+1/2k,-l]

   h'   = ( h k l ) (    -0.5    -0.5       0 )
                    (    -0.5     0.5       0 )
                    (       0       0      -1 )


Lattice unit cell after reindexing: deviation 0.73 degrees
  78.75  78.75 120.78  90.00  90.00  90.73


Number of reflections  =             10213
Number of observations =             18008
Average multiplicity =                 1.8

Resolution range in list:      47.92 ->   2.74
  
Intensity normalisation: B-factor =  -13.3

Resolution range reset to    47.92 to     3.00
   using I/sigmaI cutoff    6.0

       4 pairs rejected for E^2 too large
  

Overall CC for  6256 unrelated pairs:   0.014  N= 6256

    Estimated expectation value of true correlation coefficient E(CC) =  0.973

    Estimated sd(CC) = 1.110 / Sqrt(N)

  Number of reflections omitted from ice rings:      613
  
Estimated E(CC) of true correlation coefficient from identity =  0.973

 Failed to find spacegroup in SYMINFO!

**** Space group is not in library ****
Symop:  X,Y,Z
Symop:  Y,X,-Z
Symop:  -Y,-X,-Z
Symop:  -X,-Y,Z
Space group is not in library

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FATAL ERROR message:
Space group is not in library
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----------
From: Phil Evans


Do note that all the Pointless 1.5.x versions had a serious bug and should not be used
Phil