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Hi Mohamed,
This looks generally fine to me. One thing that stands out though is the line:
4.0- 3.5 0.79 3.23 0.24 4001 2577
where the half-dataset CC is 0.24, much greater than for lower resolutions. This suggests that something is systematically wrong in this resolution shell (or elsewhere). It may be useful to cut the data at 4 A just for this reason. As Diana points out it may be useful for other reasons as well to cut the resolution at 4 A for finding the sites.
I would suggest taking all of the datasets you have that are more or less isomorphous and putting them in a directory and then using scale_and_merge to put them all together (this is what it is designed for). It should be able to down-weight the ones that are most different from the average.
You could also try the brute-force option in phenix.hyss to try very hard to find the sites.
All the best,
Tom T
________________________________
From: mohamed noor [[email protected]]
Sent: Friday, August 07, 2015 10:55 AM
To: Terwilliger, Thomas Charles
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] Strong anomalous signal but AutoSol fails
Hi Tom
Just to check that I am on the right track, I have attached below the output from phenix.anomalous_signal using a single XDS_ASCII.HKL file from a single crystal. It is one of a few datasets, but based on Xtriage seems to be the best one.
The space group is P 3(1/2) 2 1. All datasets were collected at the peak wavelength (fluorescence scan). My initial feeling that there is a strong signal comes from CORRECT.LP. Aimless and Xtriage. IIRC, the resolution difference between the optimistic and pessimistic measurability is about 0.3-0.4 A.
Estimation of anomalous signal in a dataset
Estimating B-value for anomalous substructure as 91.2 based on
overall B-value of 75.4 (Note: you can set this with b_value_anomalous=xx)
Getting scaled data and half-datasets with scale_and_merge
Log file will be: scale.log
Files for half_dataset CC: ['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca']
Files for half_dataset CC: ['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca']
Files for half_dataset CC: ['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca']
Scaled data are in: scaled_data.mtz
Half-dataset A is in: half_dataset_a.mtz
Half-dataset B is in: half_dataset_b.mtz
Using scaled data in analysis
Setting up estimator for CC*
-------------------Summary of signal in this dataset ------------------------
Shell
CCano Nrefl Nrefl
Resolution Esqr I/sigI half anom half
47.8- 7.0 0.50 19.55 0.32 2389 2360
7.0- 6.5 0.69 10.63 0.11 621 608
6.5- 6.0 0.87 8.47 0.08 850 818
6.0- 5.5 0.88 7.52 0.08 1189 1141
5.5- 5.0 0.72 5.88 0.09 1709 1588
5.0- 4.5 0.76 4.59 0.07 2521 2247
4.5- 4.0 0.98 3.25 0.05 3881 3268
4.0- 3.5 0.79 3.23 0.24 4001 2577
3.5- 3.3 1.72 1.99 -0.02 3420 2118
Cumulative
----------------------Data quality----------------- Best guess of expected
results of finding sites
------ and phasing--------
CCano Nrefl P(Substr)
Resolution Skew Esqr half anom CC* Signal +/- (%) FOM* +/-
47.8- 7.0 0.02 0.47 0.32 2389 0.51 10.1 1.3 68 0.2 0.0
47.8- 6.5 0.02 0.50 0.28 3010 0.48 10.7 1.7 72 0.2 0.1
47.8- 6.0 0.02 0.57 0.24 3860 0.43 10.8 2.8 72 0.2 0.1
47.8- 5.5 0.05 0.64 0.20 5049 0.44 12.6 2.4 78 0.2 0.1
47.8- 5.0 0.01 0.66 0.17 6758 0.39 12.8 3.3 78 0.2 0.1
47.8- 4.5 0.01 0.69 0.14 9279 0.36 13.4 3.4 82 0.2 0.1
47.8- 4.0 0.00 0.77 0.12 13160 0.33 14.3 3.6 88 0.2 0.1
47.8- 3.5 0.00 0.77 0.15 17161 0.39 18.4 3.8 98 0.3 0.1
47.8- 3.3 0.00 0.88 0.14 20581 0.31 15.7 2.1 95 0.2 0.0
On Fri, Aug 7, 2015 at 2:30 PM, Terwilliger, Thomas Charles