[phenixbb] Phenix Xtriage label error

[Peter Zwart]

Hi,

Xtriage is not really setup to handle unmerged data, i recommend looking at
merged data instead.

Regards
Peter

On 12 April 2016 at 13:59, 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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>>>
>>
>>
>
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-- 
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P.H. Zwart
Staff Scientist
Berkeley Center for Structural Biology, Science lead
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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