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

[Stefan T. Arold]

Dear Clemens,

Thank you for the quick reply!
unfortunately, this does not fix it ... our current libxtal.sh file 
already contains exactly this function  (?!).
could it be something with the sort order ? (it says !!! WARNING, sort 
order improper !!! in the mtzutils log, and then !!! Error, too large 
indices (> 512) occur !!! !!! Fatal error while reading reflections !!! 
  - see below)

Best regards
Stefan


Clemens Vonrhein a écrit:

>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
>>
>>    
>>
>
>  
>


-- 
==================================================
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
==================================================