[phenixbb] Strong anomalous signal but AutoSol fails
mohamed noor
mohamed.noor34 at gmail.com
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.
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150809/cfa2e33e/attachment-0001.htm>
More information about the phenixbb
mailing list