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

On Tue, Apr 12, 2016 at 11:53 AM, rspencer <rspencer@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@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] On Behalf Of Alex Lee
Sent: Tuesday, April 12, 2016 11:09 AM
To: phenixbb@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@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org