[phenixbb] phenix.xtriage says that entire res range contains anomalous signal but chart says differently?
Peter Zwart
phzwart at gmail.com
Tue Aug 11 09:26:30 PDT 2009
The presence of a peak in the fluorescence doesn't guarantee low
enough standard deviations in intensities to ensure 'measurable'
anomalous differences.
How well did your crystal diffract?
The problem reported earlier is most likely a bug (which I hope can be
reproduced).
Cheers
Peter
2009/8/11, sbiswas2 at ncsu.edu <sbiswas2 at ncsu.edu>:
> Hi,
> I had similar problems recently, I did a wavelength scan of my crystal at
> the synchrotron (selenium edge) and collected one dataset at the peak
> wavelength.The scan gives me a distinct peak. However when I processed the
> data and evaluated in xtriage it says that there is no anomolous signal. I
> am unable to explain this? any advice?
> Shya
>
>
>
>
>
>
> > Uber Odd
> >
> > I reprocessed it and it seems to have resolved itself.
> >
> > Unfortunately though there seems to be no real significant anomalous
> > differences in this dataset. Back to the drawing board.
> >
> >
> > FR
> >
> > On Aug 11, 2009, at 8:54 AM, Francis E Reyes wrote:
> >
> >> 1.4-87
> >>
> >>
> >> FR
> >>
> >> On Aug 11, 2009, at 8:53 AM, Peter Zwart wrote:
> >>
> >>> which version are you using?
> >>>
> >>> P
> >>>
> >>> 2009/8/11 Francis E Reyes <Francis.Reyes at colorado.edu>:
> >>>> Hi all
> >>>>
> >>>>
> >>>> I ran xtriage on my dataset to 4.5.here's the relevant section
> >>>> pertaining to anomalous signal
> >>>>
> >>>> Analyses of anomalous differences
> >>>>
> >>>> Table of measurability as a function of resolution
> >>>>
> >>>> The measurability is defined as the fraction of
> >>>> Bijvoet related intensity differences for which
> >>>> |delta_I|/sigma_delta_I > 3.0
> >>>> min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0
> >>>> holds.
> >>>> The measurability provides an intuitive feeling
> >>>> of the quality of the data, as it is related to the
> >>>> number of reliable Bijvoet differences.
> >>>> When the data are processed properly and the standard
> >>>> deviations have been estimated accurately, values larger
> >>>> than 0.05 are encouraging.
> >>>> Note that this analyses relies on the correctness of the estimated
> >>>> standard deviations of the intensities.
> >>>>
> >>>>
> >>>> unused: - 90.6596 [ 0/1 ]
> >>>> bin 1: 90.6596 - 9.2614 [1371/1382] 0.0375
> >>>> bin 2: 9.2614 - 7.3520 [1369/1376] 0.0033
> >>>> bin 3: 7.3520 - 6.4230 [1380/1388] 0.0000
> >>>> bin 4: 6.4230 - 5.8358 [1353/1359] 0.0016
> >>>> bin 5: 5.8358 - 5.4176 [1367/1371] 0.0000
> >>>> bin 6: 5.4176 - 5.0982 [1361/1369] 0.0000
> >>>> bin 7: 5.0982 - 4.8429 [1378/1382] 0.0000
> >>>> bin 8: 4.8429 - 4.6321 [1351/1359] 0.0000
> >>>> bin 9: 4.6321 - 4.4538 [1383/1389] 0.0000
> >>>> bin 10: 4.4538 - 4.3001 [1390/1393] 0.0000
> >>>> unused: 4.3001 - [ 0/0 ]
> >>>>
> >>>> The full resolution range seems to contain a useful
> >>>> ammount of anomalous signal. Depending on your
> >>>> specific substructure, you could use all the data available
> >>>> for the location of the heavy atoms, or cut the resolution
> >>>> to speed up the search.
> >>>>
> >>>>
> >>>> If values larger than 0.05 are encouraging why is it telling me that
> >>>> the entire resolution contains a useful amount of anomalous signal?
> >>>> Did I process this incorrectly?
> >>>>
> >>>>
> >>>> 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
> >>>>
> >>>> _______________________________________________
> >>>> phenixbb mailing list
> >>>> phenixbb at phenix-online.org
> >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> -----------------------------------------------------------------
> >>> 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
> >>> -----------------------------------------------------------------
> >>>
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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
> >
> > ---------------------------------------------
> > 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
> >
>
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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
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