[sharp-discuss] Problem with TaBr phasing - including error message

Miguel Ortiz Lombardía miguel.ortiz-lombardia at afmb.univ-mrs.fr
Mon Apr 7 16:17:15 CEST 2014


Hi Thomas,

I have encountered the same problem before and if I recall it correctly
I bypassed it by removing the C-SITE lines corresponding to the Br
pseudo-atoms. Normally you collect at the Ta edge, so this is where you
get most of the signal from anyway. Otherwise, try to group the lines
corresponding to a single G-SITE, like:

C-SITES {
          C-SITE-01  G-SITE-01  Ta SPHCLUSTER  Ta6Br12:Ta
          C-SITE-02  G-SITE-01  Br SPHCLUSTER  Ta6Br12:Br
          C-SITE-03  G-SITE-02  Ta SPHCLUSTER  Ta6Br12:Ta
          C-SITE-04  G-SITE-02  Br SPHCLUSTER  Ta6Br12:Br
        ...

(Not sure this will work though)

Good luck!
Cheers,

   Miguel

Le 07/04/14 14:05, Thomas Krey a écrit :
> Dear all,
> 
> I am currently trying to phase a structure at relatively low resolution
> using a TaBr cluster.
> When using the SPHCLUSTER keyword to assign both the Ta and Br C-sites
> to the same G-site (example of the SIN file below) I get the following
> error message :
> 
>             -------------------------------------------------------------------------------------------
> 
> 
>             ERROR in subroutine READ CSITE :
> 
> 
>             -------------------------------------------------------------------------------------------
> 
> 
>             One G-site is assigned to more than one C-site
> 
>             In COMPOUND number :     2
> 
>             G-SITE number :              1
> 
> 
>             -------------------------------------------------------------------------------------------
> 
> 
>             CHECK INPUT FILE ! !
> 
> 
>             -------------------------------------------------------------------------------------------
> 
> 
> 
> 
> Here is a viw of the relevant part of the SIN file.
> 
>     G-SITES {
>        G-SITE-01 X  0.944   REFINE Y   0.329   REFINE Z   0.011   REFINE
>        G-SITE-02 X  1.096   REFINE Y   0.390   REFINE Z  -0.057   REFINE
>        G-SITE-03 X  0.811   REFINE Y   0.016   REFINE Z   0.055   REFINE
>        G-SITE-04 X  0.983   REFINE Y   0.205   REFINE Z   0.011   REFINE
>        G-SITE-05 X  1.290   REFINE Y   0.439   REFINE Z  -0.030   REFINE
>        G-SITE-06 X  1.319   REFINE Y   0.489   REFINE Z   0.004   REFINE
>        G-SITE-07 X  0.741   REFINE Y   0.072   REFINE Z   0.159   REFINE
>        G-SITE-08 X  1.383   REFINE Y   0.490   REFINE Z  -0.070   REFINE
>        G-SITE-09 X  1.339   REFINE Y   0.575   REFINE Z  -0.068   REFINE
>        G-SITE-10 X  1.345   REFINE Y   0.420   REFINE Z  -0.137   REFINE
>        G-SITE-11 X  1.444   REFINE Y   0.509   REFINE Z  -0.107   REFINE
>        G-SITE-12 X  1.086   REFINE Y   0.327   REFINE Z  -0.233   REFINE
>     }
>     COMPOUND {
>        COMPOUND-TEXT {
>           native dataset (nat)
>        }
>        C-SITES {
>        }
>        CRYSTAL {
>           CRYSTAL-TEXT {
>           }
>           T-SITES {
>           }
>           WAVELENGTH {
>              WAVELENGTH-TEXT {
>              }
>              RESOLUTION   45.13 4.20
>              BATCH {
>                 BATCH-TEXT {
>                 }
>                 SCAL_K        1.0 NOREFINE   ESTIMATE
>                 SCAL_B        0.0 NOREFINE NOESTIMATE
>                 SCAL_B6_ADD   0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE NOESTIMATE
>                 NISO_BGLO     0.0   REFINE NOESTIMATE
>                 NISO_CLOC     0.0 NOREFINE NOESTIMATE
>                 NISO_BLOC     0.0 NOREFINE NOESTIMATE
>                 NANO_BGLO     0.0 NOREFINE NOESTIMATE
>                 NANO_CLOC     0.0 NOREFINE NOESTIMATE
>                 NANO_BLOC     0.0 NOREFINE NOESTIMATE
>                 HATOM_LABEL {
>                 }
>                 OBSFILE HAP2TaS20140404-unique.data.mtz
>                 COLUMNS H=H K=K L=L FMID=FMIDnat SMID=SMIDnat 
>              }
>           }
>        }
>     }
>     COMPOUND {
>        COMPOUND-TEXT {
>           derivative 1 (Ta_peak)
>        }
>        C-SITES {
>           C-SITE-01  G-SITE-01  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-02  G-SITE-02  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-03  G-SITE-03  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-04  G-SITE-04  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-05  G-SITE-05  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-06  G-SITE-06  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-07  G-SITE-07  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-08  G-SITE-08  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-09  G-SITE-09  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-10  G-SITE-10  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-11  G-SITE-11  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-12  G-SITE-12  Ta SPHCLUSTER  Ta6Br12:Ta
>           C-SITE-13  G-SITE-01  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-14  G-SITE-02  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-15  G-SITE-03  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-16  G-SITE-04  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-17  G-SITE-05  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-18  G-SITE-06  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-19  G-SITE-07  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-20  G-SITE-08  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-21  G-SITE-09  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-22  G-SITE-10  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-23  G-SITE-11  Br SPHCLUSTER  Ta6Br12:Br
>           C-SITE-24  G-SITE-12  Br SPHCLUSTER  Ta6Br12:Br
>        }
>        CRYSTAL {
>           CRYSTAL-TEXT {
>           }
>           T-SITES {
>              T-SITE-01 {
>                 C-SITE-01
>                 HAT_OCC     1.00   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-02 {
>                 C-SITE-02
>                 HAT_OCC     0.93   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-03 {
>                 C-SITE-03
>                 HAT_OCC     0.91   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-04 {
>                 C-SITE-04
>                 HAT_OCC     0.46   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-05 {
>                 C-SITE-05
>                 HAT_OCC     0.46   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-06 {
>                 C-SITE-06
>                 HAT_OCC     0.41   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-07 {
>                 C-SITE-07
>                 HAT_OCC     0.39   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-08 {
>                 C-SITE-08
>                 HAT_OCC     0.28   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-09 {
>                 C-SITE-09
>                 HAT_OCC     0.24   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-10 {
>                 C-SITE-10
>                 HAT_OCC     0.24   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-11 {
>                 C-SITE-11
>                 HAT_OCC     0.22   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-12 {
>                 C-SITE-12
>                 HAT_OCC     0.21   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-13 {
>                 C-SITE-13
>                 HAT_OCC     1.00   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-14 {
>                 C-SITE-14
>                 HAT_OCC     0.93   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-15 {
>                 C-SITE-15
>                 HAT_OCC     0.91   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-16 {
>                 C-SITE-16
>                 HAT_OCC     0.46   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-17 {
>                 C-SITE-17
>                 HAT_OCC     0.46   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-18 {
>                 C-SITE-18
>                 HAT_OCC     0.41   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-19 {
>                 C-SITE-19
>                 HAT_OCC     0.39   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-20 {
>                 C-SITE-20
>                 HAT_OCC     0.28   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-21 {
>                 C-SITE-21
>                 HAT_OCC     0.24   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-22 {
>                 C-SITE-22
>                 HAT_OCC     0.24   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-23 {
>                 C-SITE-23
>                 HAT_OCC     0.22   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>              T-SITE-24 {
>                 C-SITE-24
>                 HAT_OCC     0.21   REFINE
>                 HAT_B      150.0 NOREFINE
>                 HAT_B6_ADD  0.0 0.0 0.0 0.0 0.0 0.0 NOREFINE
>              }
>           }
> 
> 
> 
> Any help would be greatly appreciated !!!
> 
> Thanks a lot in advance
> 
> Best
> 
> Thomas
> 
> 
> 
> 
> 
> 
> Dr. Thomas Krey
> Institut Pasteur
> Structural Virology Unit
> 25-28 Rue du Docteur Roux
> 75015 Paris
> France
> tkrey at pasteur.fr <mailto:tkrey at pasteur.fr>
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 

-- 
Miguel Ortiz Lombardía

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 86 44
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia


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