<div dir="ltr"><div><div>Hi Tom<br><br></div>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.<br><br></div>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.<br><div><br><br>Estimation of anomalous signal in a dataset<br>
<br>
Estimating B-value for anomalous substructure as 91.2 based on <br>
overall B-value of 75.4 (Note: you can set this with
b_value_anomalous=xx)<br>
<br>
Getting scaled data and half-datasets with scale_and_merge<br>
Log file will be: scale.log<br>
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Files for half_dataset CC:
['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca'] <br>
Files for half_dataset CC:
['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca'] <br>
Files for half_dataset CC:
['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca'] <br>
Scaled data are in: scaled_data.mtz<br>
Half-dataset A is in: half_dataset_a.mtz<br>
Half-dataset B is in: half_dataset_b.mtz<br>
Using scaled data in analysis<br>
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<br>
Setting up estimator for CC*<br>
<br>
-------------------Summary of signal in this dataset
------------------------<br>
<br>
Shell<br>
CCano Nrefl Nrefl<br>
Resolution Esqr I/sigI half anom half<br>
47.8- 7.0 0.50 19.55 0.32 2389 2360<br>
7.0- 6.5 0.69 10.63 0.11 621 608<br>
6.5- 6.0 0.87 8.47 0.08 850 818<br>
6.0- 5.5 0.88 7.52 0.08 1189 1141<br>
5.5- 5.0 0.72 5.88 0.09 1709 1588<br>
5.0- 4.5 0.76 4.59 0.07 2521 2247<br>
4.5- 4.0 0.98 3.25 0.05 3881 3268<br>
4.0- 3.5 0.79 3.23 0.24 4001 2577<br>
3.5- 3.3 1.72 1.99 -0.02 3420 2118<br>
<br>
Cumulative<br>
<br>
----------------------Data quality----------------- Best guess of
expected<br>
results of
finding sites<br>
------ and
phasing--------<br>
<br>
CCano Nrefl
P(Substr) <br>
Resolution Skew Esqr half anom CC* Signal +/- (%)
FOM* +/-<br>
47.8- 7.0 0.02 0.47 0.32 2389 0.51 10.1 1.3 68
0.2 0.0<br>
47.8- 6.5 0.02 0.50 0.28 3010 0.48 10.7 1.7 72
0.2 0.1<br>
47.8- 6.0 0.02 0.57 0.24 3860 0.43 10.8 2.8 72
0.2 0.1<br>
47.8- 5.5 0.05 0.64 0.20 5049 0.44 12.6 2.4 78
0.2 0.1<br>
47.8- 5.0 0.01 0.66 0.17 6758 0.39 12.8 3.3 78
0.2 0.1<br>
47.8- 4.5 0.01 0.69 0.14 9279 0.36 13.4 3.4 82
0.2 0.1<br>
47.8- 4.0 0.00 0.77 0.12 13160 0.33 14.3 3.6 88
0.2 0.1<br>
47.8- 3.5 0.00 0.77 0.15 17161 0.39 18.4 3.8 98
0.3 0.1<br>
47.8- 3.3 0.00 0.88 0.14 20581 0.31 15.7 2.1 95
0.2 0.0<br><br><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Aug 7, 2015 at 2:30 PM, Terwilliger, Thomas Charles <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Mohamed,<br>
<br>
You might try running phenix.anomalous_signal on your data (may require finding your unmerged data and running phenix.scale_and_merge first). This will give you an idea if you should be able to solve your SAD dataset.<br>
<br>
See: <a href="http://www.phenix-online.org/version_docs/1.10pre-2124/reference/anomalous_signal.html" rel="noreferrer" target="_blank">http://www.phenix-online.org/version_docs/1.10pre-2124/reference/anomalous_signal.html</a><br>
<br>
All the best,<br>
Tom T<br>
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From: <a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> [<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>] on behalf of mohamed noor [<a href="mailto:mohamed.noor34@gmail.com">mohamed.noor34@gmail.com</a>]<br>
<br>
Sent: Thursday, August 06, 2015 3:16 PM<br>
<br>
To: PHENIX user mailing list<br>
<br>
Subject: [phenixbb] Strong anomalous signal but AutoSol fails<br>
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Dear developers<br>
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I have a low resolution anomalous dataset which Aimless suggests has an effective resolution to 3.3 A and anomalous signal to 3.5 A. However, SAD phasing with AutoSol is not successful with the final R factor around 50 %.<br>
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I also have another dataset collected at a remote wavelength without anomalous signal to 3 A but they are not isomorphous (> 2 A difference in c axis).<br>
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The anomalous signal comes from the ligand heme c, which is bound covalently to the protein, so its occupancy should be 1. The protein is quite small with about 120 residues. Xtriage suggests an NCS of 6 to 20 with most likely number to be 13.<br>
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Is there any reason why a reasonable solution cannot be found? There is no twinning.<br>
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I am using the latest nightly 1.10 pre2124.<br>
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Thanks.<br>
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