[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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>>>
>>> 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
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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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