[phenixbb] phenix.xtriage says that entire res range contains anomalous signal but chart says differently?
sbiswas2 at ncsu.edu
sbiswas2 at ncsu.edu
Tue Aug 11 09:19:21 PDT 2009
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
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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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