[sharp-discuss] Symbol table not present
Derek Logan
derek.logan@mbfys.lu.se
Mon, 23 Dec 2002 15:34:31 +0100
Hi,
This did the trick, thanks! Thanks also to Marc Schiltz for pointing it
out. Now the question is how the value "undefined" got into the SIN
file?
Regards
Derek
On Monday, December 23, 2002, at 12:54 PM, Claus Flensburg wrote:
> 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