NCMI Workshops: Cryo EM Data Collection

Click the link below to watch the video

• Vaccum diagram movie

Workshop on Single Particle Reconstruction, Structural Variability and Modeling: Oct 30 - Nov 2, 2015

Presentation notes from the Workshop (some of these have not been uploaded yet)

• wah-introduction.pdf - Introduction to the Workshop and NCMI

• ludtke-overview.pdf - Workshop Overview - Steve Ludtke

• mcmullanintro.pdf - Electron Microscopes & Imaging Artifacts - Greg McMullan

• penczek-alignment.pdf - 2D Alignment Theory - Pawel Penczek

• ludtke-minitalks.pdf - CTF, Refinement, other topics - Steve Ludtke

• baldwin-orientation.pdf - Orientation and Symmetry - Phil Baldwin

• scheres-heterogeneity.pdf - Methods for Heterogeneity Analysis - Sjors Scheres

• mcmullanDetector.pdf - Direct Detector Technology - Greg McMullan

• pintilie.pdf - Chimera & Segger - Greg Pintilie

• baker-model-building.pdf - Model Building - Matt Baker

• lawson-challenges.pdf - EMDB Challenges - Cathy Lawson

Video of selected sessions Our primary video recording mechanism failed to record audio, so we unfortunately have only the EMAN and Modeling tutorials recorded

• Ludtke - Workshop Introduction

• EMAN2.12 Tutorial - Part 1 (session starts at 4:20 in video)

• EMAN2.12 Tutorial - Part 2 - 2-D Class averages

• EMAN2.12 Tutorial - Part 3 - Starting your first refinement

• EMAN2.12 Tutorial - Part 4 - Looking at the results of the first refinement

• Compositional and conformational variability in EMAN2.12 - Part 1

• Compositional and conformational variability in EMAN2.12 - Part 2

• Baker - Model building tutorial

Tutorial PDFs

• EMAN2-12_Tutorial.pdf

• EMAN2-12_Tutorial2_heterogeneity.pdf

  • Please note that e2refine_split has been improved significantly since 2.12. Suggest an update if using this method.

• Segger Tutorials

• PathwalkerGorgonTutorial.pdf

• ModelOptimizationTutorial.pdf

• ModelValidationTutorial.pdf

Tutorial Data You will also need all of the demonstration data, which we will use when going through the tutorials:

• Bgal.zip

• ribosome.zip

• segger_workshop_files.zip

• sparx_sorting.tgz

• Data-Sets.zip from Gorgon site

• sparx_ctf.tgz - NEW

• Optimize-tutorial.zip

• Validate-tutorial.zip

Completed Tutorial Projects (large files)

• Bgal-completed-tutorial.zip Result of EMAN high res tutorial (warning, 6 GB download)

• ribosome_Relion.zip Result of Relion tutorial

• Optimize_Results.zip

Software used at the workshop:

• EMAN/SPARX 2.12 (or snapshot version released after Oct. 19, 2015) - (day 1 - 2) Required. Do not use an older version.

• Relion 1.4 (optional, day 2-3) - The Relion session will largely be a demo. See comments below.

• Chimera Daily Build Oct. 17 or later - For PDB viewing and Segger tutorial (day 4, specific version required)

• Warning: we are aware of an issue with Gorgon on Ubuntu. Will remove this warning when resolved. Other Linux variants should be fine, now.

• Gorgon - Gorgon Tutorial (day 4) Please install the appropriate binary AND Data-Sets.zip

• Phenix - (end of day 4) real-space refinement of models

• LKH Solver - (day 4 - pathwalker), required only for the pathwalker tutorial, see below

• OpenMPI and PyDusa (day 2-3) SPARX tutorial may also largely be a demo, see below

CryoEM Training Workshop: June 8, 2007

Presentations

• Cryo transfer - Cruciano, Angela; Rees, Ian

• Chiu handout 1 07-06-08.ppt - Day 1 Lecture- Overview of Cryo EM - Wah Chiu

• MDS Alignment.ppt - MDS alignment - Cruciano, Angela

Workshop on Single Particle Reconstruction and Visualization: Mar. 14, 2007

Presentations

• houston_march07.ppt - EMdep: Deposition EM maps - Kim Henrick

• Chiu_EMAN Contrast theory_07_03-15.pdf - Image Contrast Theory - Wah Chiu

• 2007-EMAN-Workshop-Wen-Jiang.pdf - Icosahedral Reconstruction - Jiang, Wen

• EMANworkshop-Ferrin.pdf - Visualization tools for complex biological structures - Tom Ferrin

• chimera-eman-2007.pdf - Chimera Tutorial - Tom Goddard

• ianrees_emen2_mar8.pdf - EMEN2: An Extensible, Collaborative, Electronic Lab Notebook - Rees, Ian

• EMAN-workshop07-AIRS.ppt - VIsualizing and Analyzing CryoEM Density Maps with AIRS - Matthew Baker

• EMAN_Wkshp_MFS_Handout.ppt - Aligning and Averaging 3-D Subvolumes from Electron Cryo-Tomograms - Schmid, Michael

• Fourier Transforms.ppt - Fourier Transforms, Filtering and Convolution - Marsh, Mike

• updated_Wrks_EMAN_07.pdf - updated Image similariry measures and such - Pawel A. Penczek

• PmvVision.pdf - A Brief Introduction to PMV-VIsion - Zhao, Yong; Sanner, Michel

• EMAN_CM_Modeller.ppt - Introduction to comparative modeling with MODELLER (final version) - Webb, Ben and Topf, Maya

• EMAN_Modeller_hands_on.ppt - MODELLER hands-on session (final version) - Webb, Ben and Topf, Maya

• EMANDemo1.pdf - EMAN Practical Session Slides - Ludtke, Steven

• python_intro.pdf - Introduction to Python - Ludtke, Steven

• talk1-intro.pdf - Workshop Welcome and Single Particle Reconstruction Overview - Ludtke, Steven

• talk2-ctf.pdf - CTF Correction, Resolution Measurement & Model Bias - Ludtke, Steven

CryoEM Workshop: Oct. 17, 2006

Presentations

• 2006Oct18CryoEMCourseCCDs.ppt - Introduction To Using CCD Cameras In cryo-EM - Booth, Christopher

• CHIU Handout CryoEM Rice 06-10-18.ppt - CryoEM Lecture for Biophysics Course and Workshop on Oct 18 2006 - Wah Chiu

• Cryo TEM from specimen prep to the microscope_Gatan Presentation_LAM1.pdf - Cryo TEM from specimen prep to the microscope - Linda Melanson

• CryoEM_Imaging_NCMI_20061018.pdf - Imaging in Cryo-electron microscopy - Brink, Jaap

• Frederik.pdf - CryoEM of supsension - Professor Peter Frederik

Tutorial of TEM for Biological Cryo-Specimens: Oct. 11, 2004

Presentations

• EMtutorial.pdf - EM Tutorial (2004) - Wah Chiu

• gridClean_Li.ppt - Grid Cleaning - Zongli Li

Tutorial on CryoEM: Oct. 18, 2003

Presentations

• EM Tutorial_03_10_18.ppt - Basics of electron microscope - Wah Chiu

• EMPresentation_Glen_1018-2003.ppt - Grid for TEM - Glen Decker

• ISvitrification2003.ppt - Theory on Cryo-EM Preparation - Irina Serysheva