-----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-----
