I just realised that my reply on this issue only went to Arko, and not to the BB. I think that the problem was because of an internally out-of-synch CCP4 installation that was made available for Windows for some time. Here's my reply, which makes a similar point to David's.
===== As Tim says, you can edit the script to make it run. However, I think you've run into the problem that, for a short period of time, incompatible versions of Phaser and the ccp4i GUI were being distributed with the Windows distribution of CCP4-6.1.13. If you install CCP4-6.2, you'll have newer versions of everything and the Phaser GUI will be compatible with the executable. ===== On 12 Dec 2011, at 12:25, David Waterman wrote: > Dear Arko, > > Is it possible that your Phaser installation is out of sync with your CCP4 > installation? You might like to upgrade both. CCP4 6.2.0 includes Phaser > 2.3.0. The Phaser EP module for this release correctly writes 'SIGF(+) =' and > 'SIGF(-) =' to the LABIN line. > > Best regards > > -- David > > > On 10 December 2011 15:40, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Arko, > > your input script reads > LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) > > Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-. > > Tim > > On 12/10/2011 09:33 AM, arka chakraborty wrote: > > Hi CCPers! > > > > I have a strange problem..I am trying to obtain phases for a dna decamer > > structure from cobalt SAD data. In the Phaser EP module when I input the > > mtz generated by Ctruncate and the heavy atom PDB file generated from > > shlelxC/D and run the program it fails. Below is the log file for one of > > the runs. Plz help me out! > > > > Thanks in advance! > > > > ARKO > > > > #CCP4I VERSION CCP4Interface 2.0.7 > > #CCP4I SCRIPT LOG phaser_EP > > #CCP4I DATE 10 Dec 2011 13:45:46 > > #CCP4I USER 'UNKNOWN' > > #CCP4I PROJECT decamer > > #CCP4I JOB_ID 37 > > #CCP4I SCRATCH C:/Ccp4Temp > > #CCP4I HOSTNAME dell-pc > > #CCP4I PID 3412 > > > > <pre> > > <B><FONT COLOR="#FF0000"> > > <html><!-- CCP4 HTML LOGFILE --> > > <!--SUMMARY_BEGIN--> > > > > ##################################################################################### > > ##################################################################################### > > ##################################################################################### > > ### CCP4 PROGRAM SUITE: Phaser > > 2.2.1 ### > > ##################################################################################### > > Run time: Sat Dec 10 13:45:46 2011 > > Version: 2.2.1 > > Release Date: Tue Aug 24 18:17:37 2010 > > > > If you use this software please cite: > > $TEXT:Reference1: $$ $$ > > "Phaser Crystallographic Software" > > A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni & > > R.J. Read > > J. Appl. Cryst. (2007). 40, 658-674 > > > > $$ > > <!--SUMMARY_END--> > > <!--END--></FONT></B> > > <!--SUMMARY_BEGIN--> > > > > ************************************************************************************* > > *** Phaser Module: PREPROCESSOR > > 2.2.1 *** > > ************************************************************************************* > > > > > > <!--SUMMARY_END--> > > ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT > > <!--SUMMARY_BEGIN--> > > TITLE phasing_with_phaser_10_12_11 > > MODE EP_AUTO > > HKLIN > > "E:/block1plus2_mtzs_10_12_11/ctruncate_BLOCK1PLUS2_INTEGRATION_16_11_11.mtz" > > & > > RESOLUTION 21.659 2.900 > > HAND BOTH > > LLGCOMPLETE NCYC 50 > > LLGCOMPLETE CRYSTAL DECAMER COMPLETE ON > > LLGCOMPLETE CRYSTAL DECAMER SIGMA 6.0 > > LLGCOMPLETE CRYSTAL DECAMER CLASH DEFAULT > > LLGCOMPLETE CRYSTAL DECAMER SCATTERING ELEMENT CO > > ATOM CRYSTAL DECAMER PDB "L:/decamer/scala_NGAT-1-P1X8-pk_1_001_shelx2.pdb" > > CRYSTAL DECAMER DATASET Cobalt & > > LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) > > CRYSTAL DECAMER DATASET Cobalt & > > SCATTERING WAVELENGTH 1.60428 > > CRYSTAL DECAMER DATASET Cobalt & > > FIXDP > > COMPOSITION NUCLEIC MW 9084 NUMBER 1 > > ROOT "L:/manual_model_esrf_NG/ccp4_work/decamer_37" > > ## This script run with the command ########## > > # phaser > > ################################################ > > <!--SUMMARY_END--> > > > > -------------------- > > EXIT STATUS: SUCCESS > > -------------------- > > > > CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) > > Finished: Sat Dec 10 13:45:46 2011 > > > > </pre> > > </html> > > <pre> > > <B><FONT COLOR="#FF0000"> > > <html><!-- CCP4 HTML LOGFILE --> > > > > ##################################################################################### > > ##################################################################################### > > ##################################################################################### > > ### CCP4 PROGRAM SUITE: Phaser > > 2.2.1 ### > > ##################################################################################### > > Run time: Sat Dec 10 13:45:46 2011 > > Version: 2.2.1 > > Release Date: Tue Aug 24 18:17:37 2010 > > > > If you use this software please cite: > > $TEXT:Reference1: $$ $$ > > "Phaser Crystallographic Software" > > A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni & > > R.J. Read > > J. Appl. Cryst. (2007). 40, 658-674 > > > > $$ > > <!--END--></FONT></B> > > > > <!--SUMMARY_BEGIN--> > > ************************************************************************************* > > *** Phaser Module: READ DATA FROM MTZ FILE > > 2.2.1 *** > > ************************************************************************************* > > > > TITLE phasing_with_phaser_10_12_11 > > HKLIN > > "E:/block1plus2_mtzs_10_12_11/ctruncate_BLOCK1PLUS2_INTEGRATION_16_11_11.mtz" > > & > > RESOLUTION 21.659 2.900 > > CRYSTAL DECAMER DATASET Cobalt & > > LABIN F+ = F(+) SIGF+ > > <!--SUMMARY_END--> > > > > > > <B><FONT COLOR="#FF8800"> > > ------------------------------------------ > > SYNTAX ERROR: Use SIGFPOS SIGF(+) or SIG+ > > ------------------------------------------ > > </FONT></B> > > > > -------------------- > > EXIT STATUS: FAILURE > > -------------------- > > > > CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) > > Finished: Sat Dec 10 13:45:46 2011 > > > > </pre> > > </html> > > > > #CCP4I TERMINATION STATUS 1 > > #CCP4I TERMINATION TIME 10 Dec 2011 13:45:46 > > #CCP4I MESSAGE Task completed successfully > > > > > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFO431lUxlJ7aRr7hoRAgHbAJ469ptgbbHe28e68X6qQ5hOuznexQCcDHuR > vyl455GlQ+1gFLffPpxXxm4= > =q4ro > -----END PGP SIGNATURE----- > ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
