[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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