[phenixbb] Phenix Xtriage label error
rspencer
rspencer at uci.edu
Tue Apr 12 14:13:40 PDT 2016
Hi Alex,
Aimless is showing that there is a strong anomalous signal :
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
And also giving you a resolution cutoff for looking for the anomalous signal :
Estimate of maximum resolution for significant anomalous signal = 3.97A, from CCanom > 0.15
You have a couple of options – 1) Put the dataset in HySS and search for the Iodine (assume 1-2 iodine per molecules in your ASU) and limit the high-resolution search to 3.97.
2) go directly to Autosol and do the same resolution cutoff for searching for the anomoalous signal.
I’m sure others can also give some more detailed advice on the next steps.
Good luck!
Ryan
From: Alex Lee [mailto:alexlee198609 at gmail.com]
Sent: Tuesday, April 12, 2016 1:49 PM
To: rspencer <rspencer at uci.edu>
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Phenix Xtriage label error
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 <mailto: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> [mailto: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 <mailto: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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