[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)
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