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
--
*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
*Chennai,India*
