[phenixbb] Phenix Xtriage label error

[Billy Poon]

Hi Alex,

What are the column labels in your MTZ file? If you open your MTZ file in
the "Reflection file editor" under "Reflection tools" in the GUI, you can
see all the labels available in the file. You can also run phenix.mtz.dump
<MTZ file> at the command line.

We try to recognize standard label names, like "I(+)," "I(-)," "SIGI(+),"
and "SIGI(-)," so maybe you have labels that we do not expect. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Tue, Apr 12, 2016 at 11:53 AM, rspencer <rspencer at uci.edu> wrote:

> Hi Alex,
>
>
>
> You need to look at you anomalous signal in the aimless.log output to see
> if there was a detectable anomalous signal. You can also force iMosflm to
> treat the dataset as having an anomalous signal so that it won’t merge your
> intensities.
>
>
>
> Soaking does not guarantee that you will have an anomalous signal in your
> crystal and you may need to do a multiple crystals with increasing soak
> time to get an anomalous signal. You can easily do this by soaking the
> crystal and checking a few frames on your in-house source. Process the
> frames and see if an anomalous signal is detected.
>
>
>
> Good luck!
>
>
>
> Ryan
>
>
>
> *From:* phenixbb-bounces at phenix-online.org [mailto:
> phenixbb-bounces at phenix-online.org] *On Behalf Of *Alex Lee
> *Sent:* Tuesday, April 12, 2016 11:09 AM
> *To:* phenixbb at phenix-online.org
> *Subject:* [phenixbb] Phenix Xtriage label error
>
>
>
> Dear Phenixbb members,
>
>
>
> I have a data-set of a 8 kDa protein crystal around 2.5A resolution. The
> protein crystal was soaked in potassium iodine before collecting data using
> in-house beam (1.54A wavelength). As I expected some anomalous signal from
> the iodine ion from the crystal, after I use Imosflm to index, integrate
> and scale the data (space group P3). I got four output .mtz files:
> pointless_XXX.mtz; aimless_xxx.mtz; ctruncate_xxx.mtz;
> ctruncate_xxx-unique.mtz. After I check with viewHKL, I found the only
> unmerged mtz data is pointless_XXX.mtz, the other three mtz files are
> merged.
>
>
>
> The next step I tried to use Phenix Xtriage (Linux version 1.10.1) to
> check my mtz data for anomalous completeness, I thought in this step my mtz
> should be unmerged type to see the anomalous signal, so I chose
> "pointless_xxx.mtz" as Xtriage input, but for the data labels in the
> Xtriage GUI panel, I can only have two choices of "I, SIGI, Merged" and
> "IPR, SIGIPR, Merged", it seems I do not have a choice of an unmerged mtz
> label. I decide to leave this choice blank by choosing data labels"---".
> After I click "run", Xtriage gave an error "please select labels for input
> data".
>
>
>
> Any input on this issue?
>
>
>
> Thanks in advance.
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160412/f00b8e2e/attachment.htm>