[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>
>
>
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>
--
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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