Re: [ccp4bb] pointless question

[Robert Nolte]

An output file is created on hklout with or without the -copy flag.   The problem is why is it picking the unity matrix (solution #2) for the reindexing operator rather than the  first matrix (-h -k l) that it identifies under reindexing (which is clearly the correct answer). -----Original Message----- From: Jan Abendroth Sent: May 6, 2009 2:45 PM To: Robert Nolte Subject: Re: [ccp4bb] pointless question Hi Bob, including a -copy flag might not be totally pointless: pointless -copy hklin ... Jan 2009/5/6 Robert Nolte <rtno...@earthlink.net> I'm hoping someone can help me with a pointless problem.  I am trying to reindex data into an orientation that I used to solve the structure initially.  While I can get pointless to give me the reindexing needed to make the new data match the old data for the project, when I ask it to write the data to HKLOUT it does not carry out the reindexing. I was under the impression from the documentation it would write out the reindexed solution.  Am I doing something wrong or have I found a bug in my particular space group. I seem to recall getting this to work on a different project in the past.  I have also tried a number of different versions of pointless, and all give me the same results. The output file is shown below.  Thanks in advance for any help.        Regards,        Bob Nolte -> pointless hklin input.mtz  hklref reference.mtz hklout reindex.mtz >& pointless.log contents of pointless.log  ###############################################################  ### CCP4 6.1: POINTLESS             version 1.2.23 : 26/09/08##  ###############################################################  User: unknown  Run date: 28/ 4/2009 Run time: 13:48:05  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. OS type:      linux Release Date: 26th September 2008        ******************************************************        *                                                    *        *                     POINTLESS                      *        *                       1.2.23                       *        *                                                    *        *   Determine Laue group from unmerged intensities   *        *     Phil Evans MRC LMB, Cambridge                  *        * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*        *                                                    *        ****************************************************** --------------------------------------------------------------- Reading reference data set from file reference.mtz Maximum resolution in file reference.mtz:    1.810 Columns for F, sigF (squared to I): F_881  SIGF_881 Number of valid observations read:    18733   Highest resolution:     1.81   Unit cell:   72.66    72.66    65.98    90.00    90.00   120.00      Space group: P 3 2 1  Spacegroup information obtained from library file:  Logical Name: SYMINFO   Filename: /apps/ccp4/ccp4-6.1.0/lib/data/syminfo.lib Maximum resolution in file input.mtz:    1.870 Columns for F, sigF (squared to I): F_880  SIGF_880 Number of valid observations read:    17028   Highest resolution:     1.87   Unit cell:   72.58    72.58    66.20    90.00    90.00   120.00      Space group: P 3 2 1 Possible alternative indexing schemes   Operators labelled "exact" are exact by symmetry   For inexact options, deviations are from original cell      (root mean square deviation between base vectors)   Maximum accepted RMS deviation between test and reference cells (TOLERANCE) =  2.0                               [h,k,l]    exact                             [-h,-k,l]    exact >>>> Normalising reference dataset Log(<I>) fit for intensity normalisation: B (slope)     -18.82 >>>> Normalising test dataset Log(<I>) fit for intensity normalisation: B (slope)     -18.21 Alternative indexing relative to reference file reference.mtz $TEXT:Result:$$ $$    Alternative reindexing           CC     R(E^2)    Number Cell_deviation            [-h,-k,l]              0.967    0.092     17012      0.14             [h,k,l]               0.067    0.495     17011      0.14 $$ =============================================================== Copying merged MTZ file from input.mtz                          to reindex.mtz   Reindexing operator         [h,k,l]   Real space transformation   (x,y,z) Reindexed space group : P 3 2 1   Crystal: HKL_base   Cell:   72.58  72.58   66.2        90     90    120   Crystal: unknown   Cell:   72.58  72.58   66.2        90     90    120   17080 reflections copied to output file $TEXT:Reference: $$ Please reference $$ P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  (2005). $$ -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com