[phenixbb] Phenix Xtriage label error

[Alex Lee]

Hi Ryan,

Thank you very much!  Below are the summary of my pointless log after
"quick scale" from Imosflm (this time I force imosflm to choose P1 in the
integration and scale but pointless chose P31):

 $TEXT:Result: $$ $$

Summary data for        Project: New Crystal: New Dataset: New


                                           Overall  InnerShell  OuterShell

Low resolution limit                       82.13     82.13      2.49

High resolution limit                       2.40      8.98      2.40


Rmerge  (within I+/I-)                     0.075     0.033     0.851

Rmerge  (all I+ and I-)                    0.086     0.048     0.919

Rmeas (within I+/I-)                       0.089     0.039     1.007

Rmeas (all I+ & I-)                        0.093     0.052     0.996

Rpim (within I+/I-)                        0.047     0.021     0.534

Rpim (all I+ & I-)                         0.035     0.021     0.380

Rmerge in top intensity bin                0.031        -         -

Total number of observations              214291      4072     22139

Total number unique                        31247       617      3299

Mean((I)/sd(I))                             14.4      29.4       2.9

Mn(I) half-set correlation CC(1/2)         0.998     0.995     0.785

Completeness                               100.0      99.9      99.8

Multiplicity                                 6.9       6.6       6.7


*Anomalous completeness                      99.7      98.1      98.8*

*Anomalous multiplicity                       3.4       3.4       3.3*

*DelAnom correlation between half-sets      0.303     0.473     0.046*

*Mid-Slope of Anom Normal Probability       1.161       -         -  *


*Estimate of maximum resolution for significant anomalous signal =
3.97A, from CCanom >  0.15*


Estimates of resolution limits: overall

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  ==
maximum resolution

   from Mn(I/sd) >  1.50:                         limit =  2.40A  ==
maximum resolution

   from Mn(I/sd) >  2.00:                         limit =  2.40A  ==
maximum resolution


Estimates of resolution limits in reciprocal lattice directions:

  Along h k plane

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  ==
maximum resolution

   from Mn(I/sd) >  1.50:                         limit =  2.40A  ==
maximum resolution

  Along l axis

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  ==
maximum resolution

   from Mn(I/sd) >  1.50:                         limit =  2.40A  ==
maximum resolution


Anisotropic deltaB (i.e. range of principal components), A^2: 12.33


Average unit cell:   65.87   65.87  164.25   90.00   90.00  120.00

Space group: P 31

Average mosaicity:   0.58


Minimum and maximum SD correction factors: Fulls   1.07 104.68
Partials   1.18 134.50

Anomalous flag switched ON in input, strong anomalous signal found


$$

==============================================================


I do not know if this data set with such anomalous completeness and
multiplicity is enough for me to get phase information to

locate the Iodine, I do not have native dataset, and only have iodine
soaking dataset.



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.
>
>
>
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