data completeness

Axel T. Brunger brunger at LAPLACE.CSB.YALE.EDU
Wed Sep 11 18:53:21 EST 1996


Matthew Pugmire wrote:
> 
> I have a data set from spacegroup I222.  When I print out the completeness
> with x-plor, it is around 40%, which i am pretty sure is not right.
> Does anyone know how xplor determines the number of theoretical reflections?
> i.e. is xplor not taking into account the body centering in this case?
> anyone else seen this problem?
> 
> thanks for any info
> Matt Pugmire
> pugmire at bio.cornell.edu



X-PLOR certainly takes body-centering into account if you give it
the correct symmmetry operators.   However, all
symmetry operators must be specified (see spacegroup library).

I just ran the following example with the developmental version (3.840):


 X-PLOR>xrefin
XREFINE>a=20 b=20 c=20
XREFINE>reso 3. 50  
XREFINE>eval ($SG="I222") 
 EVALUATE: symbol $SG set to "I222" (string)
XREFINE>@XTALLIB:spacegroup.lib
 ASSFIL: file /Net/franklin/u6/xplor/xplor_sgi/xtallib/spacegroup.lib
opened.
 XREFINE>remark file  symmetry/spacegroup.lib 
 XREFINE>remark library of symmetry operators for X-PLOR 
 XREFINE>remark Jiansheng Jiang & Axel Brunger 
 XREFINE> 
 XREFINE>set echo=off end 
{ space group  23 8 "I222" ORTHORHOMBIC "mmm" "222" 71 I }
geene SYMMETRY: found symmetry operators for space group I222 in library
 XREFINE> set mess=on end 
 XREFINE> 
XREFINE>^R
generate
 XGENER: generating reflections to produce a full set
         for the specified resolution range.
         The new Fobs are set to 1 and weight
         is set to 1, all other reciprocal 
         space objects are set to 0.
 XGENE2:      106 new reflections have been generated.
XREFINE>print completeness
 XREDUC: mapping reflections into standard asymmetric unit.
 XREFIN: selected reflections will be sorted by index.
 XRTEST: number of selected reflections     106
 PRRDAT: reducing reflections
 {{  (*    resol.-range   %Completeness    %Accum.*)
   {      6.00, 50.00,   100.0000,     100.0000  }, 
   {      4.76,  6.00,   100.0000,     100.0000  }, 
   {      4.16,  4.76,   100.0000,     100.0000  }, 
   {      3.78,  4.16,   100.0000,     100.0000  }, 
   {      3.51,  3.78,   100.0000,     100.0000  }, 
   {      3.30,  3.51,   100.0000,     100.0000  }, 
   {      3.14,  3.30,   100.0000,     100.0000  }, 
   {      3.00,  3.14,   100.0000,     100.0000  }},
XREFINE>write refl fobs end
 XRTEST: number of selected reflections     106
 NREFlection=       106
 ANOMalous=FALSe { equiv. to HERMitian=TRUE}
 DECLare NAME=FOBS         DOMAin=RECIprocal   TYPE=COMP END
 INDE     2    0    0 FOBS=     1.000     0.000
 INDE     4    0    0 FOBS=     1.000     0.000
 INDE     6    0    0 FOBS=     1.000     0.000
 INDE     1    1    0 FOBS=     1.000     0.000
 INDE     3    1    0 FOBS=     1.000     0.000
 INDE     5    1    0 FOBS=     1.000     0.000
 INDE     0    2    0 FOBS=     1.000     0.000
 INDE     2    2    0 FOBS=     1.000     0.000
 INDE     4    2    0 FOBS=     1.000     0.000
 INDE     6    2    0 FOBS=     1.000     0.000
 INDE     1    3    0 FOBS=     1.000     0.000
 INDE     3    3    0 FOBS=     1.000     0.000
 INDE     5    3    0 FOBS=     1.000     0.000

-- 
=======================================================================
| Axel T. Brunger          Dept. Molecular Biophysics and Biochemistry|
| Professor/Investigator   Bass Center, 266 Whitney Avenue            |
| Office: 203-432-6143     Howard Hughes Medical Institute/Yale Univ. |
| FAX:    203-432-6946     New Haven, CT 06520, USA.                  |
| http://xplor.csb.yale.edu/~brunger                                  |
| mailto://brunger@laplace.csb.yale.edu                               |
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