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
--
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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
E-mail: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
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