Data reduction and processing tutorial

Transcription

1 Data reduction and processing tutorial Petr V. Konarev European Molecular Biology Laboratory, Hamburg Outstation BioSAXS group

2 EMBL BioSAXS beamline X33, 2012 Optics Vacuum cell Completely redesigned Efficiency gain: about 5-10 times Hutch

3 PILATUS Pixel X-ray Detector at X33 PILATUS 1M (10*100K modules) Active area 70*420 mm 2, pixel size: 170μm Readout time: 3.6ms, framing rate: 50Hz In user operation on X33 from October 2012 EMBO Course AgBeh pattern

4 BIOSAXS beamline P12 (Petra-3) Pilatus 2M Gold nanoparticles Iron oxide nanoparticles Brome mosaic virus First user samples, June 2011

5 Ag-Behenate 2D Pattern (FIT2D View)

6 Ag-Behenate 2D Pattern (with MASK)

7 Ag-Behenate 1D Pattern (FIT2D View)

8 Axis-adat Creating angular axis October 2012 EMBO Course Makeaxis dialog Angular axis file Ag-Behenate Channels

9 Raw data reduction steps Radial integration of 2D image into 1D curve Check for radiation damage, averaging of different time frames (X33: 8 frames (15 sec), P12: 20 frames (100 ms) ) Associated errors in the data points are computed from the numbers of counts using Poisson statistics Mask file is used to eliminate beamstop and inactive detector area Exact coordinates of the beam center are required for integration (determined from AgBeh data) Data are normalized to the pindiode value (intensity of the transmitted beam) Data are transferred into ASCII format containing 3 columns: s I(s) Er(s)

10 An automated SAXS pipeline at X33 / P12 Hardwareindependent analysis block Data normalization 2D-1D reduction Data processing Check for radiation damage Computation of overall parameters Database search Ab initio modelling XML-summary file generation

11 Program PRIMUS- graphical package for data manipulations and analysis data manipulations (averaging, background subtraction, merging of data in different angular ranges, extrapolation to infinite dilution ) evaluation of radius of gyration and forward intensity (Guinier plot, module AUTORG), estimation of Porod volume calculation of distance/size distribution function p(r)/v(r) (module GNOM) data fitting using the parameters of simple geometrical bodies (ellipsoid, elliptic/hollow cylinder, rectangular prism) (module BODIES) data analysis for polydisperse and interacting systems, mixtures and partially ordered systems (modules OLIGOMER, SVDPLOT, MIXTURE and PEAK) P.V. Konarev, V.V. Volkov, A.V. Sokolova, M.H.J. Koch, D.I. Svergun J.Appl. Cryst. (2003) 36,

12 PRIMUS: graphical user interface

13 PRIMUS: data processing buffer before sample: BSA 5.4 mg/ml buffer after Plot

14 PRIMUS: buffer averaging buffer before buffer after buffer averaged Average

15 PRIMUS: data processing sample: BSA 5.4 mg/ml buffer averaged Plot

16 PRIMUS: buffer subtraction sample: BSA 5.4 mg/ml buffer averaged subtracted curve Subtract

17 PRIMUS: data at different angular ranges saxs range waxs range Plot

18 PRIMUS: merging data October 2012 EMBO Course saxs range waxs range Merge

19 PRIMUS: merging data October 2012 EMBO Course saxs range waxs range merged curve Merge

20 PRIMUS: Guinier plot October 2012 EMBO Course I( s) = I(0) exp( s 2 Rg 2 3) Rg radius of gyration Rg = e-2 I0 = M MBSA*(I(0)/IBSA(0)) Guinier

21 PRIMUS: AutoRG module October 2012 EMBO Course AutoRg Petoukhov, M.V., Konarev, P.V., Kikhney, A.G. & Svergun, D.I. (2007) J. Appl. Cryst., 40, s223-s228.

22 V PRIMUS: Porod volume October 2012 EMBO Course = 2 π I ( 0 ) Q = 2 π I ( 0 ) s ( I ( s ) K ) ds 0 V = V excluded volume of particle Porod

23 Extrapolation to zero concentration

24 Merging for making final composite curve 9.3 mg/ml 1.4 mg/m 3.8 mg/ml 5.7 mg/ml 8.5 mg/mll 9.3 mg/ml 1.4 mg/m 3.8 mg/ml 5.7 mg/ml 8.5 mg/mll

25 Checking Guinier plot October 2012 EMBO Course mg/ml

26 Merging for making final composite curve 9.3 mg/ml 1.4 mg/m 3.8 mg/ml 5.7 mg/ml 8.5 mg/mll 9.3 mg/ml 1.4 mg/m 3.8 mg/ml 5.7 mg/ml 8.5 mg/mll merged

27 Real/reciprocal space transformation p(r)=r 2 γ(r) distance distribution function γ 0 (r)=γ(r)/γ(0) Probability to find a point at distance r from a given point inside the particle i r ij j

28 Distance distribution function from simple shapes

29 Distance distribution function of helix

30 PRIMUS: GNOM menu Gnom October 2012 EMBO Course Indirect Fourier Transform Run

31 PRIMUS: P(R) function Gnom October 2012 EMBO Course Indirect Fourier Transform

32 AUTOGNOM automated version of GNOM for monodisperse systems In the original version of GNOM the maximum particle size D max is a user-defined parameter and successive calculations with different D max are required to select its optimum value. This optimum D max should provide a smooth real space distance distribution function p(r) such that p(d max ) and its first derivative p'(d max ) are approaching zero, and the back-transformed intensity from the p(r) fits the experimental data. Petoukhov, M.V., Konarev, P.V., Kikhney, A.G. & Svergun, D.I. (2007) J. Appl. Cryst., 40, s223-s228.

33 Estimation of D max October 2012 EMBO Course with GNOM (under-estimation) 6.0 Poor fit to experimental data Distance distribution function p(r) goes to zero too abruptly

34 Estimation of D max October 2012 EMBO Course with GNOM (over-estimation) 12.0 Good fit to experimental data BUT: Distance distribution function p(r) becomes negative

35 Estimation of D max October 2012 EMBO Course with GNOM (correct case) 8.0 Good fit to experimental data Distance distribution function p(r) goes smoothly to zero

36 AUTOGNOM automated version of GNOM for monodisperse systems The maximum size is determined from automated comparison of the p(r) functions calculated at different D max values ranging from 2R g to 4R g, where R g is the radius of gyration provided by AUTORG. The calculated p(r) functions and corresponding fits to the experimental curves are compared using the perceptual criteria of GNOM (Svergun, 1992) together with the analysis of the behavior of p(r) function near D max and the best p(r) function is chosen for the final output. Petoukhov, M.V., Konarev, P.V., Kikhney, A.G. & Svergun, D.I. (2007) J. Appl. Cryst., 40, s223-s October 2012 EMBO Course

37 Examples for data processing Go to directory /Examples/Primus/../AgBeh - data from saxs and waxs range as well as the merged curve../bsa - standard sample for calibration of molecular mass../lysozyme example of p(r) from globular particle../lymazine example of p(r) from hollow globular (virus-like) particle../iswi_cterm example of p(r) from elongated particle