[phenixbb] xtriage

Tom Terwilliger terwilliger at lanl.gov
Wed Aug 12 10:59:35 PDT 2009


Hi Francis,

You can say:

phenix.autosol native.data=native.sca deriv.data=deriv.sca

  and wait a couple minutes until it has scaled the data (once it says  
"RUNNING HYSS" you are far enough)
and then have a look at

AutoSol_run_1_/TEMP0/dataset_1_scale.log

which will say near the end..


  isomorphous differences derivs            1  - native


  Differences by shell:

   shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE    
S/N

     1     5.000   137      29.235     0.007   1.000   0.00   0.46    
0.00
     2     3.750   201      20.277     0.011   1.000   0.09   0.31    
0.31
     3     3.500    69      16.565     0.010   1.000   0.00   0.25    
0.00
     4     3.312    80      14.804     0.009   1.000   0.00   0.23    
0.00
     5     3.125    78      14.174     0.008   1.000   0.00   0.23    
0.00
     6     3.000    81      12.567     0.010   1.000   0.00   0.20    
0.00
     7     2.875    88      12.677     0.009   1.000   0.00   0.19    
0.00
     8     2.750    94      11.249     0.012   1.000   0.09   0.18    
0.47
     9     2.625   136      11.555     0.011   1.000   0.00   0.19    
0.00
    10     2.500   126       9.975     0.011   1.000   0.00   0.17    
0.00

  Total:          1090      16.085     0.010   1.000   0.00   0.27    
0.10

(which in this particular case are not useful!)
Here R is <Fderiv-Fnative>/(2 <Fderiv+Fnative>), noise is <sigma>,
signal is sqrt(<(Fderiv-Fnative)**2>-<sigma**2>), and S/N is the ratio  
of signal to noise.

All the best,
Tom T


On Aug 12, 2009, at 11:47 AM, Peter Zwart wrote:

> I suggest using some phenix.solve utilities.
>
> xtriage isn't geared towards isomorphous diferences.
>
> Cheers
>
> Peter
>
> 2009/8/12, Francis E Reyes <Francis.Reyes at colorado.edu>:
>> Hi all
>>
>> I love the fact that xtriage can measure anomalous signal, but can it
>> also do a quick check for isomorphous differences (with and without
>> anomalous signal) similar to scalepack? Is there a phenix utility  
>> that
>> can do this?
>>
>> Thanks
>>
>> FR
>>
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>
>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>
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>>
>
>
> -- 
> -----------------------------------------------------------------
> P.H. Zwart
> Beamline Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
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