[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
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>  >>>
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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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