[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
>> >>>>
>> >>>> _______________________________________________
>> >>>> phenixbb mailing list
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>> >>>> 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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