[phenixbb] Phenix Xtriage label error

Dorothee Liebschner dcliebschner at lbl.gov
Tue Apr 12 14:38:27 PDT 2016

Hi Alex,

Your anomalous signal seems to extend to about 4 A. Xtriage will also
report a resolution limit for your useful anomalous data.

What do you mean by "merged"? Merging multiple observations of the same hkl
or averaging Friedel mates? You should use a merged file (observations) for
Xtriage (as suggested by Peter Zwart), but if you want to have some
statistics of the anomalous signal, you have to use a file where Friedel
mates are kept separate. So why don't you use your file from aimless for
xtriage? As you posted above, aimless found anomalous signal, so the output
should keep the data separate.

BTW, maybe you can extend the resolution of your data set, I/sigma is 2.9
in the highest shell. Or are you limited by detector geometry?

And as Ryan said, just try phasing/heavy atom search. No anomalous signal
indicator can tell you beforehand if phasing will be successful.

Best wishes,


On Tue, Apr 12, 2016 at 1:59 PM, Alex Lee <alexlee198609 at gmail.com> wrote:

> Hi Dorothee and Billy,
> Thank you for your information! I have both I, SIGI and IPR, SIGIPR labels
> in my unmerged MTZ (I checked this with ViewHKL). But it seems the Xtriage
> only offers choices to merged mtz. I tried to choose I,SIGI, Merged option
> (even though my mtz is unmerged), the Xtriage output shows "anomalous flag
> false" and I did not get any additional anomalous information from the
> report.
> On Tue, Apr 12, 2016 at 12:16 PM, Dorothee Liebschner <
> dcliebschner at lbl.gov> wrote:
>> Hi Alex,
>> What data labels are in the file pointless_xxx.mtz?
>> You can check with
>> > phenix.mtz.dump pointless_xxx.mtz
>> The output should list the available labels.
>> (you should see the labels also in hklview)
>> You cannot leave the data labels choice blank in xtriage, as you have two
>> data choices in your file, so you need to tell the program which ones to
>> use.
>> Apart from xtriage, it is always helpful to check the anomalous signal
>> reported in various log files from your data processing steps, such as
>> aimless.log and also from mosflm (I am not familiar to mosflm but I guess
>> it outputs also some info about anomalous signal?).
>> Best wishes,
>> Dorothee
>> On Tue, Apr 12, 2016 at 11:08 AM, Alex Lee <alexlee198609 at gmail.com>
>> wrote:
>>> 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.
>>> _______________________________________________
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