[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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