mrc software for 2d crystal structure determination n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
MRC software for 2d crystal structure determination PowerPoint Presentation
Download Presentation
MRC software for 2d crystal structure determination

Loading in 2 Seconds...

play fullscreen
1 / 17

MRC software for 2d crystal structure determination - PowerPoint PPT Presentation


  • 130 Views
  • Uploaded on

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.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

MRC software for 2d crystal structure determination


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
mrc software for 2d crystal structure determination

MRC software for 2d crystal structure determination

  • Introduction
  • Basic Functions and Principles

Henderson & Unwin (1975) Nature 257, 28-32

history
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
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 and

C 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

3D reconstruction from 2D TEM images

Unwin, Scientific America

single image processing
Single Image Processing

Unbending

MMBOX

Boxing

Fourier Transform

unbending is possible because distortion can be tracked along the lattices
Unbending is possiblebecause distortion can be tracked along the lattices

QUADSERCHK

The distortion is plotted at 10x the actual values

reference from rough 3d reconstruction

Correlation against perfect crystalline structure gives distortion map

Reference from rough 3D reconstruction

MAKETRAN

Cross Correlation

Reference from best region in the image

determine amplitudes and phases of diffraction spots mmbox ttbox ctfapply
Determine Amplitudes and Phases of Diffraction spots MMBOX / TTBOX + CTFAPPLY

Amos, Henderson & Unwin (1982) Prog. Biophys. molec. Biol., 39, 183-231

h k Amp Phase IQ Background

0 1 434.9 34.2 3 156.8

0 2 7924.5 44.6 1 148.5

0 3 1373.7 210.6 1 158.3

0 4 1411.4 228.4 1 124.3

0 5 710.5 206.4 2 106.3

0 6 1870.8 126.0 1 121.1

.

.

.

relationship between amplitude and phase error
Relationship between Amplitude and Phase Error

IQ values

  • determined by amplitudes
  • Used as measure of phase error

Im

IQ~2

IQ~4

Re

image2000/source/mmboxa.for

merging information and refinement

Merging information and Refinement

ORIGTILT

LATLINE

Unwin, Scientific America

origtilt program
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, baxes
    • Rotation
    • Flip crystal upside down
    • Defocus inversion
lattice line fitting latlinek
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 167,849-852

a=D

D

a

=

1

Stahlberg

latlinek parameters

ALAT = c in 3D xtal lattice parameter

LATLINEK Parameters

RCUT

DELPRO

PFACT

protein density

  • AK, IWF, IWP for weighting of amp error vs. phase error of the fit.

D=RMAX-RMIN

RMAX

REAL SPACE

RMIN

BINSIZE

FOURIER SPACE

1/ALAT

DELPLT

1/D

GENERATE CURVE, FIT STATS, and FIT SAMPLE

GUESS

SAMPLE CURVE for PLOT

avoid mistakes
Avoid mistakes

Good Bad

  • Unbending
    • Reference should look like perfect crystalline structure
  • Exacting Phase/Amplitude
    • Real signal should become significant when added up

5-3.5 A

777 7 7

8 7 6 7 7

777 7 6

7 8 7 7 7

777 7 7

8-6 A

789 9 8

7 10 13 11 7

8 8 11 11 8

7 7 10 11 9

7 79 9 8

  • 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

10Å

what mrc package can not do
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
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