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----- >
