[phenixbb] xtriage

Francis E Reyes Francis.Reyes at Colorado.EDU
Wed Aug 12 11:20:09 PDT 2009


Tom	


This is great.


Do you have a table from a good derivative?

Thanks

FR

On Aug 12, 2009, at 11:59 AM, Tom Terwilliger wrote:

> 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
>>>
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>>>
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>>>
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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
>> BCSB:     http://bcsb.als.lbl.gov
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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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> cbss
>
>
>
>
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---------------------------------------------
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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