[phenixbb] phenix reindex

Peter Zwart PHZwart at lbl.gov
Mon Jul 12 13:17:44 PDT 2010


yes,  it is possible to do this in phenix. I am not sure if CCP4 can handle
this case.

the way to do it in phenix is to use phenix.reflection_file_converter and
assign a new space group  ( P 43 (a+b,-a+b,c)   ) and ask to remove all
integral absences. Subsequently you move to the standard setting (P43 with
small cell).

try this maybe


phenix.reflection_file_converter original.sca --space_group='P 43
(a+b,-a+b,c)'   --eliminate-invalid-indices --sca=step1.sca

phenix.reflection_file_converter step1.sca
--change-of-basis=to_reference_setting --sca=done.sca


There might be a step missing, send me the full logfile off-list and i'll
fill you in.


HTH

Peter



2010/7/12 Gregor Hagelueken <gregorhagelueken at gmail.com>

> Hi,
>
> I got the following output from phenix.xtriage:
>
> ...
> The full list of Patterson peaks is:
>
> x      y      z            height   p-value(height)
> ( 0.500, 0.500, 0.000 ) :   27.056   (2.355e-03)
> ( 0.333,-0.488, 0.000 ) :    4.790   (9.454e-01)
>
> If the observed pseudo translationals are crystallographic
> the following spacegroups and unit cells are possible:
>
> space group                operator         unit cell of reference setting
>  P 43 (a+b,-a+b,c)       x+1/2, y+1/2, z  (83.41, 83.41, 42.64,  90.00,
> 90.00, 90.00)
> ...
>
> I know I can use REINDEX in CCP4 to reindex the data, but is there a way to
> do it in phenix?
>
> Cheers,
> Gregor
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>



-- 
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P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
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