[sharp-discuss] solvent flattening error in p61 and p6522

[Clemens Vonrhein]

Dear Stefan,

this is a 'feature' of awk under IRIX. Solution

1. edit the file $BDG_home/lib/libxtal.sh and find the line that
   starts with

ismtz () {


2. change the whole function to

ismtz () {
  if [ $# -eq 1 ]; then
    chkfil $1
    # awk on IRIX complains about 'Input record too long'
    #ismtz_tmp=`head -1 $1 | awk '{print $1}' | grep -c MTZ`
    ismtz_tmp=`head -1 $1 | grep -c MTZ`
    if [ $ismtz_tmp -eq 0 ]; then
      echo 1
    else
      echo 0
    fi
  fi
}

This should fix it under IRIX ...

Cheers

Clemens

On Tue, Jul 05, 2005 at 05:37:57PM +0200, Stefan T. Arold wrote:
> Dear all,
> 
> Using autoSHARP (sharp2.0.4. for irixn32, sushi 3.2.3.) in P61 and in 
> P6522 we run into the following errors during the solvent flattening 
> step : (see below)
> 
> Thanks for any suggestions and/or workarounds!!
> 
> Best regards
> Stefan
> 
> 
> 
> 
> 1. Automatic density modification (original hand)
>    (details) - assuming 1 molecule in asymmetric unit :
> UX:awk: ERROR: Record `VERS MTZ:V1.1 TITLE ...' has too many fields 
> UX:awk: INFO: Input record number 30512 UX:awk: INFO: Source line number 2
> /RX2/progs/sharp/bin/sharp/uniqueify.sh[125]: test: argument expected
> 
> 
> [click on 'details'] gives:
> 
>       2.1.1 Using solvent content 63.0 %
>    (details)
> 
>  ERROR   : unable to determine correlation!
> 
> [click on 'details'] gives:
> 
> /RX2/progs/sharp/bin/sharp/solomon.sh[2228]: 473776 Memory fault
>  ERROR: unable to substract FH/PHIH from Fmodori/PHImodori!
>         Have a look in solo_63.0pc/t_sftools_cycle1.log
> 
> [click on 'solo_63.0pc/t_sftools_cycle1.log'] gives:
> 
> 
> 
> OPTIONS ARE:
> 
>     ABSENT      MODE      CALC  CHECKHKL  COMPLETE    CORREL
>     DELETE    EXPAND       FFT    FOURPT    HLCONV       I2F
>       LIST       MAP    MAP2SF     MAPIN  MAPLIMIT    MAPOUT
>    MAPSTAT     MERGE   OPTION1   PHASHFT      PLOT     PURGE
>       READ    REDUCE   REINDEX     RFREE    SELECT       SET
>       SORT      STOP    WINDOW     WRITE
> 
> >> give your option (or hit <return> to list options)
> 
> selected: MODE
> 
> 
>   SFTOOLS is now in BATCH mode
> 
> >> give your option (or hit <return> to list options)
> 
> selected: READ
> 
> 
> 
>  OPENED INPUT MTZ FILE
>  Logical Name: solo_63.0pc/t_mtzutils_4_cycle1.mtz   Filename: 
> solo_63.0pc/t_mtzutils_4_cycle1.mtz
> 
> 
> Reading file : solo_63.0pc/t_mtzutils_4_cycle1.mtz 
> 
> With format  : MTZ
> 
>   !!! WARNING, sort order improper !!!
> 
>   Sort order will be set to 1 2 3
>   Use option SORT [h k l] later if needed
> The following columns will be read:
> 
> TYPE  LABEL
> ===========
> 
>   F   FP 
> 
>   Q   SIGFP 
> 
>   P   PHIcent 
> 
>   W   FOM 
> 
>   A   HLA 
> 
>   A   HLB 
> 
>   A   HLC 
> 
>   A   HLD 
> 
>   F   FH 
> 
>   P   PHIH 
> 
>   F   FCmapori 
> 
>   P   PHICmapori 
> 
>   F   FCmapoff 
> 
>   P   PHICmapoff 
> 
>   F   DELFWT 
> 
>   P   PHDELFWT 
> 
>   F   Fmodoff 
> 
>   P   PHImodoff 
> 
>   W   FOMCMB1 
> 
>   P   PHCMB1 
> 
>   I   NUMORB 
> 
>   F   Fmodori 
> 
>   P   PHImodori 
> 
>   !!! Error, too large indices (> 512) occur !!!
>   !!! Fatal error while reading reflections !!!
>             0 reflections read successfully
>   Trying to clean up the mess
>   Deleting new columns
>   Deleting new reflections
> 
>  give READ HELP to get more information
> 
> 
> >> give your option (or hit <return> to list options)
> 
> 
> OPTIONS ARE:
> 
>     ABSENT      MODE      CALC  CHECKHKL  COMPLETE    CORREL
>     DELETE    EXPAND       FFT    FOURPT    HLCONV       I2F
>       LIST       MAP    MAP2SF     MAPIN  MAPLIMIT    MAPOUT
>    MAPSTAT     MERGE   OPTION1   PHASHFT      PLOT     PURGE
>       READ    REDUCE   REINDEX     RFREE    SELECT       SET
>       SORT      STOP    WINDOW     WRITE
> 
> >> give your option (or hit <return> to list options)
> 
> selected: CALC
> 
> 
>   Destination column created with label:
>  Ftmp
> 
>   Destination column created with label:
> 
>  PHItmp
>   !!! WARNING, column label does not exist !!!
> 
>   Check spelling or use the column number
> 
>   Check your spelling and/or use option:
>   LIST LABELS to get a list of valid names
> 
>  give CALC HELP to get more information
> 
> 
> >> give your option (or hit <return> to list options)
> 
> selected: DELETE
> 
> 
>   WARNING: no columns specified
> 
>  give DELETE HELP to get more information
> 
> 
> >> g
> 
> -- 
> ==================================================
> Stefan T. Arold, PhD
> Centre de Biochimie Structurale
> UMR 50848 CNRS - UMR 554 INSERM - UM1
> Faculte de Pharmacie
> 15, Av. Charles Flahault
> F-34093 Montpellier CEDEX 5
> email: S.Arold at cbs.cnrs.fr
> Phone: +33 (0)4.67.04.34.34
> Fax:   +33 (0)4.67.52.96.23
> ==================================================
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 

-- 

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* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
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