 |
 |
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: [log in to unmask] > Subject: [ccp4bb] pointless error > To: [log in to unmask] > > 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--> >