[phenixbb] xtriage

Tom Terwilliger terwilliger at lanl.gov
Wed Aug 12 11:26:17 PDT 2009


Hi Francis,

Here is a table for a good derivative. Note that the S/N is very  
high...but this includes
non-isomorphism. It only means that the differences between native and
derivative are well-measured.

  isomorphous differences derivs            1  - native


  Differences by shell:

   shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE    
S/N

     1     5.600  1018     285.012     0.287   0.998 105.05  26.73    
3.93
     2     4.200  1386     324.927     0.216   1.000  84.78  26.76    
3.17
     3     3.920   542     330.807     0.214   1.002  85.00  28.36    
3.00
     4     3.710   523     286.487     0.237   1.002  81.31  27.29    
2.98
     5     3.500   662     282.383     0.235   1.001  75.58  37.12    
2.04
     6     3.360   518     255.782     0.241   1.003  72.69  27.18    
2.67
     7     3.220   630     237.778     0.253   1.000  68.87  29.94    
2.30
     8     3.080   727     208.271     0.255   1.000  61.39  29.19    
2.10
     9     2.940   897     190.044     0.254   0.999  42.78  42.99    
1.00
    10     2.800  1067     169.022     0.280   0.999  50.54  33.24    
1.52

  Total:          7970     256.096     0.245   1.000  75.29  31.41    
2.48

-Tom T

On Aug 12, 2009, at 12:20 PM, Francis E Reyes wrote:

> 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
>>>>
>>>> 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
>>> 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
>> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb


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
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




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