mrc software for 2d crystal structure determination
DESCRIPTION
MRC software for 2d crystal structure determination. Introduction Basic Functions and Principles. Henderson & Unwin (1975) Nature 257, 28-32. History. Developed over 30 yrs by a number of people Written in Fortran image2010 image format compatible with ccp4 plots in postscript format. - PowerPoint PPT PresentationTRANSCRIPT
MRC software for 2d crystal structure determination
Henderson & Unwin (1975) Nature 257, 28-32
• Introduction
• Basic Functions and Principles
History Developed over 30 yrs by a number of people Written in Fortran image2010
image format compatible with ccp4 plots in postscript format
http://www.tonh.net/museum/plotter.html
Documentation Crowther, Henderson and Smith (1996)
J. Struct. Biol.116, 9-16 Docs in the package: image2010/doc/ Docs on 2dx.org Help Docs in 2dx applications
C LATLINPRESCAL : program to correct image amplitudes for effects of CTF andC to calculate appropriate weights for output to LATLINE. C******************************************************************************** C Control cards: C C Card 1: NSER,ZMIN,ZMAX (*) C serial number on ORIGTILT input C and ZSTAR limits to be passed on to LATLINE. C Card 2: IQMAX (*) C maximum value of IQ for spots to be used C C INPUT file is raw file straight from ORIGTILT : on unit FOR001 C OUTPUT has the format required by LATLINE : on unit FOR003 C C*******************************************************************************
3D reconstruction from 2D TEM images
Unwin, Scientific America
Single Image Processing
Unbending
Boxing MMBOX
Fourier Transform
Unbending is possiblebecause distortion can be tracked along the lattices
The distortion is plotted at 10x the actual values
QUADSERCHK
Reference from rough 3D reconstruction
MAKETRAN
Reference from best region in the image
Cross Correlation
Correlation against perfect crystalline structure gives distortion map
Determine Amplitudes and Phases of Diffraction spots MMBOX / TTBOX + CTFAPPLY
h k Amp Phase IQ Background0 1 434.9 34.2 3 156.8 0 2 7924.5 44.6 1 148.50 3 1373.7 210.6 1 158.30 4 1411.4 228.4 1 124.30 5 710.5 206.4 2 106.30 6 1870.8 126.0 1 121.1 .
.
.
Amos, Henderson & Unwin (1982) Prog. Biophys. molec. Biol., 39, 183-231
IQ values determined by
amplitudes Used as measure of
phase error
Relationship between Amplitude and Phase Error
Re
Im
IQ Amp/(RMS background) cutoff
Phase Error
1 8.18 7
2 4.09 14
3 2.73 21
4 2.05 28
5 1.64 35
6 1.36 42
7 1.17 49
8 1.02 56
image2000/source/mmboxa.for
IQ~4
IQ~2
Merging information and Refinement
Unwin, Scientific America
ORIGTILTLATLINE
ORIGTILT program Move the projection images (i.e., phase origins) to a
common center and compatible orientation
Reference Symmetry special position Last set of merged image Last calculated 3D model
Refine Phase origin Tilt geometry Beam Tilt
Standardize a, b axes Rotation Flip crystal upside
down Defocus inversion
Lattice line fitting (LATLINEK) model fitting in the reciprocal space of the continuous
line in the non-repeating (z*) direction based on the assumption that the density in the real space is limited by a window function
Agard (1983) JMB 167,849-852a=D
=
D
1
a
Stahlberg
LATLINEK Parameters
RMIN RMAX
RCUT
PFACTprotein density
ALAT = c in 3D xtal lattice parameterDELPRO
BINSIZE
D=RMAX-RMIN
GUESS GENERATE CURVE, FIT STATS, and FIT SAMPLE
SAMPLE CURVE for PLOT
REAL SPACE
1/D DELPLT
1/ALATFOURIER SPACE
AK, IWF, IWP for weighting of amp error vs. phase error of the fit.
Importance of Defining Correct Window Function Width
D=260 A D=100 A
y=a0+a1xy=a0+a1x+a2x2
Avoid mistakes Unbending
Reference should look like perfect crystalline structure
Good Bad
Exacting Phase/Amplitude Real signal should become
significant when added up
Merging/Refinement Projected symmetry should be
obvious in untilted image and its Fourier transform
Choose window function width according to property of the specimen
8 IQ8 spot does not make the result as reliable as 1 IQ1 spot
8-6 A7 8 9 9 87 10 13 11 78 8 11 11 87 7 10 11 97 7 9 9 8
5-3.5 A
7 7 7 7 78 7 6 7 77 7 7 7 67 8 7 7 77 7 7 7 7
5 Å
7 Å10 Å
What MRC package can not do Make your first crystal Merging results from different crystal form Untwist Rotational disorder in the crystal Correct for bending perpendicular to the
membrane Merging information from unknown and variable
number layers of stacked crystals ….
Take this home: Computers have
changed but the principle is the same.
Keep a critical eye during the process while enjoying the express ride of 2dx and IPLT.
A 1947 or prior photograph (cropped) of IBM (Hollerith) operators at the Caltech Computing Center machine room performing crystallographic computation using the IBM card punch systems as described in Shaffer et al. (1946) and briefly summarized in Swift (1947).
http://journals.iucr.org/a/issues/2008/01/00/sc5015/sc5015bdy.html