Do note that all the Pointless 1.5.x versions had a serious bug and should not be used Phil
On 19 Nov 2011, at 09:49, Rajesh kumar wrote: > 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 > > Date: Tue, 15 Nov 2011 09:17:34 -0500 > From: ccp4...@hotmail.com > Subject: [ccp4bb] pointless error > To: CCP4BB@JISCMAIL.AC.UK > > 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 > > <!--SUMMARY_BEGIN--> > <B><FONT COLOR="#FF8800"> > <!--SUMMARY_END--> > ------------------------------ > > FATAL ERROR message: > Space group is not in library > ------------------------------ > <!--SUMMARY_BEGIN--> > </FONT></B> > <!--SUMMARY_END--> >
