Re: [phenixbb] xtriage

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 ), noise is <sigma>, signal is sqrt(<(Fderiv-Fnative)**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 :

...

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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-- ----------------------------------------------------------------- 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 PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net ----------------------------------------------------------------- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] 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