[phenixbb] Strong anomalous signal but AutoSol fails

Sun Aug 9 03:39:45 PDT 2015

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.

On Sun, Aug 9, 2015 at 11:37 AM, mohamed noor <mohamed.noor34 at gmail.com>
wrote:

> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> 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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