[phenixbb] Strong anomalous signal but AutoSol fails

Sun Aug 9 03:37:04 PDT 2015

Hi Tom

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.

I also tried to run Phaser/MRage in all possible SG within both point
groups without any luck.

Mohamed

On Fri, Aug 7, 2015 at 10:26 PM, Terwilliger, Thomas Charles <
terwilliger at lanl.gov> wrote:

> 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 [mohamed.noor34 at gmail.com]
> *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 <
> terwilliger at lanl.gov> wrote:
>
>> Hi Mohamed,
>>
>> 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.
>>
>> See:
>> http://www.phenix-online.org/version_docs/1.10pre-2124/reference/anomalous_signal.html
>>
>> All the best,
>> Tom T
>>
>>
>>
>>
>>
>> From: phenixbb-bounces at phenix-online.org [
>> phenixbb-bounces at phenix-online.org] on behalf of mohamed noor [
>> mohamed.noor34 at gmail.com]
>>
>> Sent: Thursday, August 06, 2015 3:16 PM
>>
>> To: PHENIX user mailing list
>>
>> Subject: [phenixbb] Strong anomalous signal but AutoSol fails
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>>
>> Dear developers
>>
>>
>>
>>
>> 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 %.
>>
>>
>>
>>
>>
>> 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).
>>
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> Is there any reason why a reasonable solution cannot be found? There is
>> no twinning.
>>
>>
>>
>>
>> I am using the latest nightly 1.10 pre2124.
>>
>>
>>
>>
>> Thanks.
>>
>>
>>
>>
>>
>>
>
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