[sharp-discuss] pkmaps invalid keyword

Clemens Vonrhein vonrhein at globalphasing.com
Fri Jan 5 08:38:26 GMT 2007


Hi Mike,

you could try and patch the file

  $BDG_home/bin/sharp/autoSHARP/resid.sh

by hand, changing line 1132 from

    [ `echo $comb | egrep -c "^[ ]*\(|\)[ ]*$"` -eq 0 ] && comb="( $comb )"

to

    [ `echo $comb | egrep -c "^[ ]*\(|\)[ ]*$"` -eq 0 ] && [ `echo $comb | awk '{print NF}'` -ne 0 ] && comb="( $comb )"

The next release should not show this issue.

Cheers

Clemens

On Thu, Jan 04, 2007 at 06:24:54PM -0500, brent3 at sas.upenn.edu wrote:
> Hello,
> 
> I'm getting the same error message with pkmaps as the October 25th post,
> "Invalid sub-keyword in position 2". I have attached the LISTautoSHARP.html
> file. I get the message when running autoSHARP on derivatives (MIR/SIR)
> containing anomalous differences. AutoSHARP on MAD/SAD datasets works fine.
> 
> Are there any patches or ways around this problem?
> 
> Thanks,
> Mike
> 

> 
>                                autoSHARP run
>                        (Project MIRAS28, User brent)
>                                [Sushi 3.4.0]
> 
>                     (start: Thu Jan 4 15:24:49 EST 2007)
>      _________________________________________________________________
> 
>  Copyright (C) 1999-2005 Clemens Vonrhein and the
>                          Buster Development Group.
> 
>                All rights reserved.
> 
>     Use of this program implies acceptance of conditions
>     given in the SHARP licence agreement.
> 
>     (please reload this document from time to time!)
> 
>     Please cite:
>       Vonrhein, C, Blanc, E., Roversi, P and Bricogne,
>       G. (2005). Automated structure solution with autoSHARP. In
>       "Crystallographic Methods", S Doublie, Ed., Humana Press,
>       Totowa, NJ, submitted.
> 
>      Title : running  autoSHARP  on  MIRAS  data  using  S184C  and S193C
>    derivatives
>      _________________________________________________________________
> 
>                                 1. Preparation
>      _________________________________________________________________
> 
>      1.1 Checking supplied information
> 
>       [1](details)    [2](explanation)    [[3]2, [4]3]    (2 seconds)
> 
>                 2 warnings :
>      * [5]No # of residues
>      * [6]CCP4 version unsupported
> 
>              2 important notes (out of ~ 14) :
>      * [7]Speed/Accuracy rate set to 5
>      * [8]116 amino acid residues in sequence
>      _________________________________________________________________
> 
>      1.2 Converting files
> 
>       [9](details)    [10](explanation)    (8 seconds)
>      _________________________________________________________________
> 
>      1.3 Extracting additional information
> 
>       [11](details)     [12](explanation)    [[13]4, [14]5, [15]6]    (10
>    seconds)
> 
>                   2 important notes (out of ~ 29) :
>      * [16]most likely 2 molecules and solvent fraction of 0.553
>      * [17]overall resolution = 30.00 2.80 Å
>      _________________________________________________________________
> 
>      1.4 Collecting and analysing all data
> 
>       [18](details)    [19](explanation)    (24 seconds)
> 
>                 1 warning :
>      * [20]Unusual ABS(DANO)/FMID ratio for 1 reflexion
>        (DANOS184C/FS184C)
> 
>      _________________________________________________________________
> 
>      1.5 Adding test set column
> 
>       [21](details)    [22](explanation)    [[23]7]    (11 seconds)
> 
>                   3 notes :
>      * [24]Low anomalous completeness of 78% (derivative 1)
>      * [25]Low completeness of 84% (derivative 2)
>      * [26]Low anomalous completeness of 79% (derivative 2)
>      _________________________________________________________________
> 
>                             2. Using unscaled data
>      _________________________________________________________________
> 
>      2.1 Scaling of merged data
> 
>       [27](details)    [28](explanation)    (20 seconds)
> 
>                 1 warning :
>      * [29]serious differences between datasets
> 
>      _________________________________________________________________
> 
>      2.2 Additional analysis (NCS, sequence ...)
> 
>       [30](details)    [31](explanation)    [[32]8, [33]9]    (1 minute 7
>    seconds)
>      _________________________________________________________________
> 
>                         3. Using merged and scaled data
>      _________________________________________________________________
> 
>      3.1 Finding sites
> 
>       [34](details)     [35](explanation)     [[36]10]     (53 minutes 58
>    seconds)
> 
>                   1 important note (out of ~ 30) :
>      * [37]trial 1 (derivative 1 SIRAS - 4 sites): CC(E) = 0.297
>      _________________________________________________________________
> 
>                         4. Using list of initial sites
>      _________________________________________________________________
> 
>      4.1 Create a SIN file
> 
>       [38](details)      [39](explanation)      [[40]11,   [41]12]     (1
>    second)
>      _________________________________________________________________
> 
>      4.2 Run first round of SHARP
> 
>       [42](details)      [43](explanation)      [[44]12,   [45]11]     (6
>    minutes 23 seconds)
> 
>                   5 notes :
>      * [46]figure-of-merit [acentric/centric] = 0.21405/0.28257
>      * [47]Compound 2 : phasing power ISO [acentric/centric] =
>        1.203/1.041
>      * [48]Compound 2 : phasing power ANO = 0.219
>      * [49]17 cycles
>      * [50]results (maps) available
>      _________________________________________________________________
> 
>      4.3 Cycling between residual map interpretation and SHARP
> 
>          4.3.1 Automatic interpretation of residual maps    [51](details)
>       [52](explanation)    (3 seconds)
>  ERROR   : (see    [53]RESID/LISTautoSHARP.html)
>      _________________________________________________________________
> 
> 
>     [54]Buster Development Group
> 
> Verweise
> 
>    1. http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html
>    2. http://maya:8080/manual/autoSHARP3.html#checks
>    3. file://localhost/tmp/LISTautoSHARP.html#CCP4
>    4. file://localhost/tmp/LISTautoSHARP.html#MerrittXXXX
>    5. http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html#WarningNum1
>    6. http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html#WarningNum2
>    7. http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html#NoteNum1
>    8. http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html#NoteNum4
>    9. http://maya:8080/users/brent/logfiles/MIRAS28.0/CONVERT/LISTautoSHARP.html
>   10. http://maya:8080/manual/autoSHARP3.html#convert
>   11. http://maya:8080/users/brent/logfiles/MIRAS28.0/GETINFO/LISTautoSHARP.html
>   12. http://maya:8080/manual/autoSHARP3.html#getinfo
>   13. file://localhost/tmp/LISTautoSHARP.html#Wilson1942
>   14. file://localhost/tmp/LISTautoSHARP.html#Matthews1968
>   15. file://localhost/tmp/LISTautoSHARP.html#Kantardjieff2003
>   16. http://maya:8080/users/brent/logfiles/MIRAS28.0/GETINFO/LISTautoSHARP.html#NoteNum23
>   17. http://maya:8080/users/brent/logfiles/MIRAS28.0/GETINFO/LISTautoSHARP.html#NoteNum26
>   18. http://maya:8080/users/brent/logfiles/MIRAS28.0/COLLECT/LISTautoSHARP.html
>   19. http://maya:8080/manual/autoSHARP3.html#collect
>   20. http://maya:8080/users/brent/logfiles/MIRAS28.0/COLLECT/LISTautoSHARP.html#WarningNum1
>   21. http://maya:8080/users/brent/logfiles/MIRAS28.0/UNIQUEIFY/LISTautoSHARP.html
>   22. http://maya:8080/manual/autoSHARP3.html#uniqueify
>   23. file://localhost/tmp/LISTautoSHARP.html#Bruenger1992
>   24. http://maya:8080/users/brent/logfiles/MIRAS28.0/UNIQUEIFY/LISTautoSHARP.html#NoteNum1
>   25. http://maya:8080/users/brent/logfiles/MIRAS28.0/UNIQUEIFY/LISTautoSHARP.html#NoteNum2
>   26. http://maya:8080/users/brent/logfiles/MIRAS28.0/UNIQUEIFY/LISTautoSHARP.html#NoteNum3
>   27. http://maya:8080/users/brent/logfiles/MIRAS28.0/SCALEIT/LISTautoSHARP.html
>   28. http://maya:8080/manual/autoSHARP3.html#scaleit
>   29. http://maya:8080/users/brent/logfiles/MIRAS28.0/SCALEIT/LISTautoSHARP.html#WarningNum1
>   30. http://maya:8080/users/brent/logfiles/MIRAS28.0/ANALYSE/LISTautoSHARP.html
>   31. http://maya:8080/manual/autoSHARP3.html#analyse
>   32. file://localhost/tmp/LISTautoSHARP.html#RossmannBlow1962
>   33. file://localhost/tmp/LISTautoSHARP.html#Epp1971
>   34. http://maya:8080/users/brent/logfiles/MIRAS28.0/SHELX/LISTautoSHARP.html
>   35. http://maya:8080/manual/autoSHARP3.html#shelx
>   36. file://localhost/tmp/LISTautoSHARP.html#Schneider2002
>   37. http://maya:8080/users/brent/logfiles/MIRAS28.0/SHELX/LISTautoSHARP.html#NoteNum30
>   38. http://maya:8080/users/brent/logfiles/MIRAS28.0/MKSIN/LISTautoSHARP.html
>   39. http://maya:8080/manual/autoSHARP3.html#mkSIN
>   40. file://localhost/tmp/LISTautoSHARP.html#BricogneVonrheinFlensburgSchiltzPaciorek2003
>   41. file://localhost/tmp/LISTautoSHARP.html#Fortelle1997
>   42. http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html
>   43. http://maya:8080/manual/autoSHARP3.html#sharp
>   44. file://localhost/tmp/LISTautoSHARP.html#Fortelle1997
>   45. file://localhost/tmp/LISTautoSHARP.html#BricogneVonrheinFlensburgSchiltzPaciorek2003
>   46. http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum1
>   47. http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum2
>   48. http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum3
>   49. http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum4
>   50. http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum5
>   51. http://maya:8080/users/brent/logfiles/MIRAS28.0/RESID/LISTautoSHARP.html
>   52. http://maya:8080/manual/autoSHARP3.html#resid
>   53. http://maya:8080/users/brent/logfiles/MIRAS28.0/RESID/LISTautoSHARP.html
>   54. http://www.globalphasing.com/

> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/sharp-discuss


-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************



More information about the sharp-discuss mailing list