Hi Tim,
yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL
intensities as amplitudes, producing very different output statistics,
compared both to the XDS statistics and to an mtz file with amplitudes
created from that XDS file. I've contacted a phenix developer a few
weeks ago, but got no reply, yet (maybe, my e-mail got lost).
Cheers,
Dirk.
Am 03.07.2014 13:46, schrieb Tim Gruene:
> Hi Dirk,
>
> that would truely be very sad - the XDS file format is such a beautiful,
> self-contained and well documented format for diffraction data that a
> misinterpretation should really not happen.
>
> Cheers,
> Tim
>
> On 07/03/2014 01:42 PM, Dirk Kostrewa wrote:
>> ... and please check, whether phenix.xtriage recognized the input data
>> as intensities or as amplitudes.
>> In case of doubt, convert the intensives first into an mtz file with Fs
>> instead of Is and run phenix.xtriage on the mtz file.
>>
>> Best regards,
>>
>> Dirk.
>>
>> Am 03.07.2014 13:36, schrieb Tim Gruene:
>>> Hi Yamei,
>>>
>>> did you by any chance feed the output file from XDS into xtriage? It
>>> would indicate the data were twinned even for a near perfect insulin
>>> test crystal. After discussion with the developers I understand that
>>> phenix does not seem to handle unmerged data well.
>>>
>>> With phenix.xtriage V. phenix-1.9-1692:, XDS_ASCII.HKL
>>> Mean |L| :0.392 (untwinned: 0.500; perfect twin: 0.375)
>>> Mean L^2 :0.219 (untwinned: 0.333; perfect twin: 0.200)
>>>
>>> after pointless and merging with aimless:
>>> Mean |L| :0.492 (untwinned: 0.500; perfect twin: 0.375)
>>> Mean L^2 :0.322 (untwinned: 0.333; perfect twin: 0.200)
>>>
>>> As workaround, run the data through pointless/aimless first.
>>>
>>> Best,
>>> Tim
>>>
>>> On 07/03/2014 05:04 AM, Yamei Yu wrote:
>>>> HI all,
>>>>
>>>> I have a data set processed to P42 21 2 (the space group was
>>>> suggested by pointless ). then I use phenix.xtriage to analysis the
>>>> data. I was confused by the phenix.xtriage result.
>>>> According to the following number it is twin data, but why it
>>>> couldn’t find any possible twin law?
>>>>
>>>> Determining possible twin laws.
>>>>
>>>> 0 merohedral twin operators found
>>>> 0 pseudo-merohedral twin operators found
>>>> In total, 0 twin operator were found
>>>>
>>>>
>>>> Mean |L| :0.378 (untwinned: 0.500; perfect twin: 0.375)
>>>> Mean L^2 :0.205 (untwinned: 0.333; perfect twin: 0.200)
>>>>
>>>>
>>>> How could be that? Is it twin or no twin?
>>>>
>>>> Please find the log file of phenix.xtrage in attachment.
>>>>
>>>> Thank you so much for your suggestion!
>>>>
>>>>
>>>> ************************************************
>>>>
>>>> Yamei Yu
>>>>
>>>>
--
*******************************************************
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
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