[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
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