[sharp-discuss] Symbol table not present
Claus Flensburg
sharp-discuss@globalphasing.com
Mon, 23 Dec 2002 11:54:26 +0000
Hi Derek,
the crash is caused by the 'undefined' argument on the STRATEGY card.
Try and set that card to read:
STRATEGY 7 15 63 63 63 127 127 127 127
Hmm, it looks like you've just added sites 8, 13-17 - so perhaps
CYCLES 10 6 9
STRATEGY 7 15 63 63 63 7 15 23 63
is better. It means:
6) Occ
7) Occ + xyz
8) Occ + B
9) Occ + xyz + B
Greetings,
ClAuS
On Mon, Dec 23, 2002 at 11:32:31AM +0100, Derek Logan wrote:
> 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
>
>
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