[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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