[phenixbb] xtriage

sbiswas2 at ncsu.edu sbiswas2 at ncsu.edu
Tue Aug 11 10:14:35 PDT 2009


Hi,
Crystals diffracted to 2.8A, does it have anything to do with scaling? I
did use the anomolous feature in HKL2000.
Shya



> 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
>>  >>>>
>>  >>>> _______________________________________________
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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
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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
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>>  >
>>
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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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