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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Mohamed,
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<div>I don't know of any way to know the number of copies in the ASU exactly, no.</div>
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<div>It does seem that the solutions you have found so far are not likely to be correct, as you suggest. Here is one more general approach to try: as you have a high degree of NCS, try to use it to evaluate your solutions. I assume there is 1 Fe per molecule.
With high NCS in the crystal, it is likely (but not for sure) that the molecules in the ASU have some kind of symmetric arrangement. So you could look at any potential substructure solutions you find and see if there is any symmetry in the sites. You can
just look at them in Coot with symmetry turned on or you can use phenix.find_ncs to look for NCS in the sites.</div>
<div><br>
</div>
<div>Additionally you could calculate a rotation function from your native data and from your anomalous differences and see if there are NCS rotation axes that are present (for example a 13-fold rotation axis or something like that).</div>
<div><br>
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<div>All the best,</div>
<div>Tom T</div>
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<div id="divRpF566739" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> mohamed noor [mohamed.noor34@gmail.com]<br>
<b>Sent:</b> Sunday, August 09, 2015 4:39 AM<br>
<b>To:</b> Terwilliger, Thomas Charles<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] Strong anomalous signal but AutoSol fails<br>
</font><br>
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<div></div>
<div>
<div dir="ltr">One more thing, is there any way of knowing how many copies there should be in the ASU? Right now, I am doing it blindly as there is a huge range based on Matthew's coefficient calculation.<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Aug 9, 2015 at 11:37 AM, mohamed noor <span dir="ltr">
<<a href="mailto:mohamed.noor34@gmail.com" target="_blank">mohamed.noor34@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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<div>Hi Tom<br>
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When I used data in P 3(2)21, Hyss returned a CC of 0.2 for 10 sites and in P 3, I obtained a CC of 0.32 for 17 sites (out of 20 requested). From the documentation, CC 0.2 is considered possible and 0.3 is good. However, this does not translate into good models
built by AutoBuild with the R factor being in the 45-50 % and low model CC (0.25). The FOM in AutoSol also seems to not reflect what it should be even if it is better than 0.4. Interestingly, when I input a dataset with low anomalous signal to 5 A (out of
3.5 A), I got an FOM of > 0.4 and Bayes-CC of 45 - but bad model.<br>
<br>
</div>
I also tried to run Phaser/MRage in all possible SG within both point groups without any luck.<span class="HOEnZb"><font color="#888888"><br>
<br>
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<span class="HOEnZb"><font color="#888888">Mohamed<br>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Aug 7, 2015 at 10:26 PM, Terwilliger, Thomas Charles
<span dir="ltr"><<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span> wrote:<br>
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<div>Hi Mohamed,</div>
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<div>This looks generally fine to me. One thing that stands out though is the line:</div>
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<div>4.0- 3.5 0.79 3.23 0.24 4001 2577</div>
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<div>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.</div>
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<div>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.</div>
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<div>You could also try the brute-force option in phenix.hyss to try very hard to find the sites.</div>
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<div>All the best,</div>
<div>Tom T</div>
<div><font face="Times" size="3"><br>
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<div style="direction:ltr"><font face="Tahoma" color="#000000" size="2"><b>From:</b> mohamed noor [<a href="mailto:mohamed.noor34@gmail.com" target="_blank">mohamed.noor34@gmail.com</a>]<br>
<b>Sent:</b> Friday, August 07, 2015 10:55 AM<br>
<b>To:</b> Terwilliger, Thomas Charles<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] Strong anomalous signal but AutoSol fails<br>
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<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>
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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>
<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>
Files for half_dataset CC: ['TEMP4/XDS_ASCII_SG150_1800frames_reprocFriedel_0_1.sca']
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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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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>
<br>
<br>
<br>
<br>
<br>
From: <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>] on behalf of mohamed noor [<a href="mailto:mohamed.noor34@gmail.com" target="_blank">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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