[sharp-discuss] problem running shelx on autoSHARP

ISHII Ryohei ishii at biochem.s.u-tokyo.ac.jp
Wed May 24 15:35:39 BST 2006


Hi all,

I receive the following error message and the program is stopped 
in the running shelxc/shelxd using autoSHARP on Linux Fedora Core 3 and CCP4 5.0.
I use the reflection file from scalepack and select unmerged (internally scaled) data as the Entry Point.

----------------------------------------------------------------------
 
     2.1.2 SHELXD - searching for 10 sites    (details) 
      2.1.3 Cycle 1    (details) 
(skipping)
Try     7, CC All/Weak   51.79 / 28.58, best 51.79 / 28.90, best PATFOM  8.06 [  11 sites]   (details)
Try     7, CC All/Weak   51.79 / 28.58, best 51.79 / 28.90, best PATFOM  8.06 [  11 sites]   (details)
Try    12, CC All/Weak   51.97 / 28.87, best 51.97 / 28.90, best PATFOM  8.06 [  11 sites] /usr/local/sharp2/bin/sharp/autoSHARP/libautoSHARP.sh: line 1646: 23035 Done                    prepcards "LABI $2" "RESO $autoSHARP_RSTATS_reso" "$autoSHARP_RSTATS_extra" "$autoSHARP_RSTATS_extra2" "END"
     23038 Segmentation fault      | $autoSHARP_RSTATS_exe hklin $1 hklout $aSid_mtz >>$aSid_log 2>&1
 ERROR   : (see    RSTATS_1_SAD_1_10.12.11.log)

The last few lines in RSTATS_1_SAD_1_10.12.11.log is as follows:
-------------------------------------------------------------------
 Analysis done on Signed ( not absolute) values of FP and Fc
 Data line--- WIDTH_OF_BINS RTHETA 0.000788
 Data line--- END
>From ccp4_lrassn: expected type F does not match file type E for column E

  Resolution limits for scaling:      3.800    35.380 Angstrom
   corresponding limits in 4(sin theta/lambda)**2:    0.00080   0.06925
  Bin Width:    0.0008

  ALL reflections now written to output mtz file

  Resolution limits for final statistics :     3.800    35.380 (A)

  Width of ranges on Fo before scaling:        0.0
  Initial Scale factor (for Fc): K     =      1.00000
  Initial B factor:         TempFactor =    0.00000
  Maximum Number Cycles of refinement:     0
  Print out only on Final Cycle
  Output file contains Fp,Fc,  [SigFp,SigFc,phi,free,wt]
  Scale and B determined by minimizing :
              Sum{ w(Fo-K*exp(-Bs)*Fc)**2 }
  Scale and B will be applied to Fcalc
          (and to sig(Fcalc) if given)
----------------------------------------------------------------------

Any help will be greatly appreciated!
Thank you for advance.

ISHII Ryohei

************************************************
ISHII Ryohei, Ph. D.

RIKEN Genomic Science Center

Department of Biophysics and Biochemistry
Graduate School of Science, University of Tokyo

E-mail  :  ishii at biochem.s.u-tokyo.ac.jp
TEL     :  +81-3-5841-4394
FAX     :  +81-3-5841-8057
************************************************

 




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