[phenixbb] phenix.xtriage says that entire res range contains anomalous signal but chart says differently?
Frank von Delft
frank.vondelft at sgc.ox.ac.uk
Thu Aug 13 01:04:26 PDT 2009
Sounds like you killed the signal during collection. Radiation damage
is the most common cause of (probable) failure of SAD experiments (see
e.g. James Holton's analyses).
Try using fewer images of your dataset, that might help. And look at
B-factor decay in scaling, if it's more than 5A**2, you're almost
certainly screwed (but no guarantees if it's less.)
phx.
sbiswas2 at ncsu.edu wrote:
> 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
>>>> 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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