[sharp-discuss] Symbol table not present
Derek Logan
derek.logan@mbfys.lu.se
Mon, 23 Dec 2002 11:32:31 +0100
Hi,
What is happening if SHARP crashes immediately on running with the
following error?
forrtl: severe (59): list-directed I/O syntax error, unit -5, file
Internal List-Directed Read
Symbol table not present, doing non-symbolic traceback
0: [0x1201dbb3c]
1: [0x1201dc15c]
2: [0x1201d50d4]
3: [0x1201d4208]
4: [0x12012ea70]
5: [0x1200c0d68]
6: [0x120146320]
7: [0x120171f64]
8: [0x120034c98]
I'm doing a bit of sulphur SAD on lysozyme (otherwise called reinventing
the wheel). What I've done is to extract Hendrickson-Lattmann
coefficients from an earlier run of solvent flattening and I'm trying to
re-refine the HA positions using these phases. Another thing is that
it's impossible to use the SIN afterwards in SUSHI. I just get a blank
window. The SIN file looks like this:
DATAFILES /usr/local/xtal/sharp/users/derek/sharpfiles/datafiles
TITLE Lysozyme real sites SF phases
OBSFILE Lyso13.2_solo_45.0pc.data.mtz
LEVEL ADVANCED
MODE REFINE RESIDUAL ELECTRON_DENSITY
CYCLES 10 6 9
REJECT YES 5
NUM_BINS 8
USE_ABCD REFINE
STRATEGY 7 15 63 63 undefined 127 127 127 127
WEED 1 0.5 3
CELL 78.107 78.107 37.146 90.000 90.000 90.000
SYMMETRY P43212
ATOMS {
C 628.
N 174.
O 192.
S 7.
}
G-SITES {
G-SITE-01 X -0.116627 REFINE Y 0.274143 REFINE Z 0.088820
REFINE
G-SITE-02 X -0.015751 REFINE Y 0.378646 REFINE Z 0.313204
REFINE
G-SITE-03 X 0.064601 REFINE Y 0.171555 REFINE Z 0.708341
REFINE
G-SITE-04 X -0.024421 REFINE Y 0.193645 REFINE Z 0.793208
REFINE
G-SITE-05 X 0.082953 REFINE Y 0.153549 REFINE Z 0.707075
REFINE
G-SITE-06 X -0.001494 REFINE Y 0.190975 REFINE Z 0.740508
REFINE
G-SITE-07 X -0.007263 REFINE Y 0.374434 REFINE Z 0.377551
REFINE
G-SITE-08 X -0.125087 REFINE Y 0.291100 REFINE Z 0.142720
REFINE
G-SITE-09 X -0.080665 REFINE Y 0.260768 REFINE Z 0.376679
REFINE
G-SITE-10 X -0.067617 REFINE Y 0.349623 REFINE Z 0.540225
REFINE
G-SITE-11 X -0.138607 REFINE Y 0.373202 REFINE Z 0.334579
REFINE
G-SITE-12 X 0.131693 REFINE Y 0.138153 REFINE Z 0.869853
REFINE
G-SITE-13 X -0.090765 REFINE Y 0.132379 REFINE Z 0.330696
REFINE
G-SITE-14 X -0.011805 REFINE Y 0.304606 REFINE Z 0.104588
REFINE
G-SITE-15 X 0.061733 REFINE Y 0.053896 REFINE Z 0.773528
REFINE
G-SITE-16 X 0.040793 REFINE Y 0.175033 REFINE Z 1.027185
REFINE
G-SITE-17 X 0.237879 REFINE Y 0.124209 REFINE Z 0.647982
REFINE
}
COMPOUND {
COMPOUND-TEXT {
}
C-SITES {
C-SITE-01 G-SITE-01 S
C-SITE-02 G-SITE-02 S
C-SITE-03 G-SITE-03 S
C-SITE-04 G-SITE-04 S
C-SITE-05 G-SITE-05 S
C-SITE-06 G-SITE-06 S
C-SITE-07 G-SITE-07 S
C-SITE-08 G-SITE-08 S
C-SITE-09 G-SITE-09 S
C-SITE-10 G-SITE-10 S
C-SITE-11 G-SITE-11 S
C-SITE-12 G-SITE-12 S
C-SITE-13 G-SITE-13 S
C-SITE-14 G-SITE-14 S
C-SITE-15 G-SITE-15 S
C-SITE-16 G-SITE-16 S
C-SITE-17 G-SITE-17 S
}
CRYSTAL {
CRYSTAL-TEXT {
}
T-SITES {
T-SITE-01 {
C-SITE-01
HAT_OCC 0.76435 REFINE
HAT_B 34.16589 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-02 {
C-SITE-02
HAT_OCC 0.16915 REFINE
HAT_B 14.85581 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-03 {
C-SITE-03
HAT_OCC 0.96493 REFINE
HAT_B 36.19373 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-04 {
C-SITE-04
HAT_OCC 1.00000 REFINE
HAT_B 30.83000 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-05 {
C-SITE-05
HAT_OCC 0.56853 REFINE
HAT_B 27.62336 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-06 {
C-SITE-06
HAT_OCC 0.19844 REFINE
HAT_B 19.73557 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-07 {
C-SITE-07
HAT_OCC 0.35430 REFINE
HAT_B 19.02480 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-08 {
C-SITE-08
HAT_OCC 1.00000 REFINE
HAT_B 30.00000 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-09 {
C-SITE-09
HAT_OCC 0.39171 REFINE
HAT_B 16.64677 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-10 {
C-SITE-10
HAT_OCC 0.77151 REFINE
HAT_B 27.49979 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-11 {
C-SITE-11
HAT_OCC 0.61530 REFINE
HAT_B 30.26318 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-12 {
C-SITE-12
HAT_OCC 0.76911 REFINE
HAT_B 66.32101 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-13 {
C-SITE-13
HAT_OCC 1.00000 REFINE
HAT_B 30.00000 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-14 {
C-SITE-14
HAT_OCC 1.00000 REFINE
HAT_B 30.00000 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-15 {
C-SITE-15
HAT_OCC 1.00000 REFINE
HAT_B 30.00000 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-16 {
C-SITE-16
HAT_OCC 1.00000 REFINE
HAT_B 30.00000 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
T-SITE-17 {
C-SITE-17
HAT_OCC 1.00000 REFINE
HAT_B 30.00000 REFINE
HAT_B6_ADD 0.000 0.000 0.000 0.000 0.000
0.000 NOREFINE
}
}
WAVELENGTH {
WAVELENGTH-TEXT {
}
RESOLUTION 57.801 1.600
BATCH {
BATCH-TEXT {
}
SCAL_K 0.77728 NOREFINE
SCAL_B 0.00000 NOREFINE
SCAL_B6_ADD 1.504 0.000 1.504 0.000 0.000
-3.009 NOREFINE
NISO_BGLO 0.00000 NOREFINE
NISO_CLOC 0.00000 NOREFINE
NISO_BLOC 0.00000 NOREFINE
NANO_BGLO 0.00000 NOREFINE
NANO_CLOC 0.00000 NOREFINE
NANO_BLOC 0.00000 NOREFINE
HATOM_LABEL {
S ATOM_f' 0.2571 NOREFINE ATOM_f" 0.3756 NOREFINE
}
COLUMNS H=H K=K L=L FMID=F_new SMID=SIGF_new DANO=DANO_new
SANO=SIGDANO_new ISYM=ISYM_new
}
}
}
}
END
Any ideas?
Happy Christmas or synchronous religious festival
Derek