[sharp-discuss] Symbol table not present
Clemens Vonrhein
vonrhein@globalphasing.com
Sat, 28 Dec 2002 14:01:31 +0000
Hi Derek,
> 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?
Good question: did you prepare the SIN file through the SIN file
editor? Did you run Sushi 3.0.15? Could you send me the SIN file you
used (end_SomeThing.1.sin probably ... or new_SomeThing.1.sin) to
create the SomeThing.2.sin file. this way I could try to find the
problem and fix it.
Cheers
Clemens
>
> 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
>
>
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park Tel: +44-(0)1223-353033
* Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************