Site map

An overview of the available content on this site. Keep the pointer still over an item for a few seconds to get its description.

• news
  • Pages on 2dx/MRC data flow available
  • Movie on 3D merging available
  • Workshop on Electron Crystallography of Membrane Proteins announced
  • 2dx Version 3.0.0 released
  • 2dx_merge in beta available
  • 2dx_merge Movie Tutorial available
  • 2dx_merge and Maximum Likelihood will be released soon
  • 2dx Version 2.1.0 released
  • 2dx Version 2.0.0 released
  • 2dx Tutorial now available as movie
  • 2dx Manual now available
  • 2dx software released
  • Electron Crystallography Workshop 2006
  • 3D merging test data available
  • Workshop Photos, Slides, Movies available
  • 2dx_3.1.2 available
• structures
  • 2dstructs.pdf
• workshop
  • 2006
    • Presentations
    • Program
    • Workshop Flyer
    • Program (PDF)
    • Local Organization
    • Movies
  • 2008
    • Program (HTML)
    • Participants
    • Photos
      • ECW2008-GroupPhoto.jpg
      • ECW2008-Names.jpg
      • Iban-Talk-1.jpg
      • Iban-Talk-2.jpg
      • Iban-Talk-3.jpg
      • Iban-Talk-4.jpg
      • IPLT-Practical-1.jpg
      • IPLT-Practical-2.jpg
    • Program (PDF)
    • Travel Info
    • UC-Davis-Map.jpg
    • Practicals flash videos
    • Registration
    • Speaker PDF Notes Drop-Box
      • Glaeser - Fourier theory: 2D
      • Glaeser - Contrast formation in the TEM
      • IBAN Ubarretxena - Journal of Structural Biology 2007 Vink.pdf
      • Werner.tar.gz
      • Glaeser - Beam-induced movement: resolution loss
      • Glaeser - TEM: Instrumentation for high resolution data collection
      • Gipson - HIO 2
      • Gipson - HIO 1
      • Catherine Vénien-Bryan - Lipids and their properties
      • 2D crystallization by dialysis
      • Stahlberg-Sept12-2008.pdf
      • Stahlberg-Sept11-2008.pdf
      • Michael Landsberg - Landsberg_JSB_2007.pdf
      • Iban Ubarretxena-Belandia - high throuhput 2dx screening
      • Anchi Cheng - AnchiCheng3DmergingHandOut.pdf
      • Andreas Schenk - visualization.ppt
      • Gipson - HIO 3
      • AnchiChengBootstrap Resamplinghandout.pdf
      • Andreas Schenk - Simulation and correction of crystal distortions.ppt
      • ECW2008 - 2dx Intro - Notes.pdf
      • Anchi Cheng MRC for 2dx image
      • Michael Landsberg - Landsberg detergent v7.pdf
    • Videos for the 2008 Electron crystallography workshop
      • Carbon sandwich
      • Back injection Method
      • 3D reconstruction
      • Hybrid Input Output Algorithm
      • Calculation of the variance of a 3D map by the bootstrap method
      • Basel System for 2D crystal screening
      • High performance cameras for electron crystallography (GATAN)
      • IPLT software Introduction
      • Symmetry
      • Beam-induced resolution loss
      • Fourier theory-2D
      • 2D crystal screening
      • Effect of unbending before vs. after CTF correction
      • IPLT software Difraction processing
      • Lipids and their properties
      • Detergents chelation and dilution
      • Data collection
      • Detergents and their properties
      • Sample preparation
      • Merging in 2DX
      • Data collection - Diffraction
      • TEM- Instrumentation for high resolution data collection
      • Monolayer approach and biobeads
      • Image Processing in 2D- MRC software for real-space images
      • 2DX software - Introduction
      • Electron detection- DQE, MTF, Scanner vs. Film, CMOS, deceleration CCD
      • Dialysis
      • Contrast formation in the TEM- Phase Shifting devices, aberration vs aberration correction
      • Molecular mechanisms of membrane transport studied by cryo-EM
      • Merging with the MRC software
• documentation
  • 2dx Movies
  • Sample Prep Movies
    • Cryo-EM Sample Preparation
    • Gyobu-Sandwich.mov
    • Cryo-EM Sample Preparation, mp4
    • XVIVO Scientific Animation
    • harvard.flv
    • Quicktime Movie Player
    • 2D-cryst-Fourier.mov
    • See also the Tutorial Movies for 2dx_image
  • MRC Software
    • MRC Documentation
      • emrefs.doc
      • emindex.doc
      • ann2000
      • image.doc
      • plot2k.doc
    • Electron Crystallography
      • Step 3
      • Step 5
      • Step 4
      • Step 1
      • Step 2
      • Step 6
    • Symmetry
    • Electron Diffraction Processing Introduction
    • MRC Headers
      • backauto
      • allspace
      • ccunbendk
      • latline
      • label
      • avrgamphs
      • fftrans
      • maketran
      • ctfapplyk
      • ctffind2
      • boximage
      • masktran
      • latlinprescal
      • convdeconv
      • mmboxa
      • mmlatref
      • origtiltk
      • ctffind
      • rfiltim
      • padbox
      • ctftilt
      • pickprofk
      • pickauto
      • ttboxk
      • syncfitp3
      • twofile
      • scalimamp3d
      • ttrefine
      • ttmask
      • taperedge
      • quadserchk
      • ttboxref
      • twolatt
    • MRC File Format
    • ReStructuredText
    • Tilt Geometry Definition
    • MRC programs
      • LABEL
      • HISTO
      • BOXIMAGE
      • TAPEREDGE
      • AUTOCORRL
      • TWOFILE
      • FFTRANS
      • CTFAPPLY
      • QUADSERCHB
      • CCUNBENDE
      • ORIGTILTD
      • TTMASK
      • TTBOX
      • MMBOXA
      • MASKTRANA
      • PREPMKMTZ
      • AVRGAMPHS
      • LATLINE
      • ALLSPACE
  • Frequently Asked Questions
  • 2dx Software
    • Publications
    • Known Bugs
      • mrc2tif / tif2mrc
      • 2dx and spaces in the directory path
    • Manual
      • ML algorithm applied to 2d crystals
      • Refining a lattice
      • Processing an individual image
      • Explanation of the 2dx GUI
      • The Full-Screen Image Navigator
      • Refining the CTF
      • Beginning an Image Processing Project
      • Spot Selection
      • Data Flow
        • Processing in 2dx_image of ONE image
        • Merging in 2dx_merge in 2D
        • Merging in 2dx_merge in 3D
      • Status Pane
    • Parameters
      • allspace
      • beamtilt
      • contrast
      • create mask info
      • csandkv
      • ctfplotresmax
      • defocus
      • domask
      • imagename and non-masked imagename
      • imagenumber
      • imageorigin
      • imagesidelength
      • latevaluate
      • lattice
      • magnification and digitizer step size
      • masking
      • merging
      • minmax
      • ml
      • periodogram
      • phacon
      • phaori
      • real cell
      • refine
      • resolution
      • rotrev
      • spidermap
      • spotlist
      • spots
      • symmetry
      • tempkeep
      • tiltgeometry
      • treatspotscan
      • ttfcorfirst
      • ttrefine
      • unbend
      • backup
      • cleanup
      • tilt
      • downscale
      • Crop
      • Comment
      • initialization
      • inventory
      • Zstar
    • Screen Shots
      • Full-Screen-Browser-1.jpg
      • Unbend1.jpg
      • Polygon-Selection.jpg
      • Calc-FFT.jpg
      • Life-FFT.jpg
      • Spot-Selection.jpg
      • Zoom.jpg
      • Update.jpg
      • Direct-Manual-1.jpg
      • Direct-Manual-2.jpg
      • Full-Screen-Browser-2.jpg
      • Unbend-1.jpg
    • Movie Tutorials
      • Version 3.0: 2dx_merge 2D merging
        • Quicktime Movie Player
        • 2dx_merge-merging.mov
      • Version 2.0: 2dx_image Primer Movie
        • 2dx_image-primer.mov
        • Quicktime Movie Player
      • Version 3.0: 2dx_merge GUI
        • 2dx_merge-GUI.mov
        • Quicktime Movie Player