NCMI Workshops: Cryo EM Image Processing

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

Cryo-EM Workshop at the National University of Singapore: July 9 - July 13, 2012

Presentations

• emviz.pdf - Map Visualization with Chimera - Tom Goddard

• CHIU CryoEM lecture NUS workshop 2012.pdf - CryoEM Basics - Wah Chiu

• Model_bias.pdf - Model Bias- Mini Lecture Quantitative - Steve Ludtke

• Particle_Eval.pdf - Particle Analysis (mini-lecture) - Steve Ludtke

• EMAN2_Intro.pdf - EMAN2 Introduction - Steve Ludtke

• Single_Particle_Intro.pdf - Introduction to Single Particle Analysis - Steve Ludtke

• Lu Gan NUS cryo-ET lecture.pdf - Cryo-ET Basics - Lu Gan

• Slides_for_workshop3_handout_red.pdf - Single Particle Tomography slides/handout - Michael Schmid et al

• Flagella01-07-10-2012_red.pdf - Trypanosome Flagella - Schmid, M, Koyfman AY, Gheiratmand L, Fu CJ, Khant HA, Huang D, He CY, Chiu W

• CHIU CryoEM Modeling NUS-reduced.pdf - CHIU Modeling Lecture - Wah Chiu

Structural & Computational Biomedical Informatics and Cryo-EM (UK): June 8 - June 12, 2009

Presentations

• workflow_tutorial_final.pdf - EMAN2 Workflow Tutorial (Revised) - Steve Ludtke

• Workshop_1.pdf - Introduction to Single Particle Reconsruction and EMAN2 - lecture notes - Steve Ludtke

Workshop on Single Particle Reconstruction, Map Interpretation and Visualization: Dec 10 - Dec 13, 2008

Presentations

• Ludtke_1.pdf - Introduction to Single Particle Reconsruction and EMAN2 - Steve Ludtke

• workflow_tutorial.pdf - EMAN2 Workflow Tutorial - David Woolford

• Python_1.pdf - Introduction to Python - Steve Ludtke

• berman-NCMI-dec08.ppt - What the Protein Data Bank teaches us about structural biology - Berman, Helen M.

• Wrks_EMAN2_08.pdf - Introduction - Penczek, Pawel

• 2008-EMAN-Wen-Jiang.pdf - Near-atomic resolution 3-D reconstruction of viruses - Jiang, Wen

• 2008-12-11 NCMI Baylor Workshop 60min.pdf - Integrating Diverse Data for Structure Determination of Macromolecular Assemblies - Andrej Sali

EMAN/Single Particle Tutorial: June 11, 2008

Presentations

• Talk1.pdf - Introduction to Single Particle Reconstruction in EMAN1 - Steve Ludtke

• Talk2-ctf.pdf - Introduction to Fourier Transforms and CTF Correction - Steve Ludtke

• Demo1.pdf - Demo session containing walkthrough for EMAN1 DVD - Steve Ludtke

• fits.pdf - FFT's Part 1 (more detailed lecture) - Steve Ludtke

• ffts2.pdf - FFT's Part 2 (more detailed lecture) - Steve Ludtke

Grand challenges for Nanomedicine and Nanobiology: Aug 27, 2007

Presentations

• ACS poster.ppt - Single-walled Carbon Nanotubes in the Intact Organism:Near-IR Imaging and Biocompatibility Studies in Drosophila - Beckingham, Kathleen

• collaboration.ppt - Surfaces/nanopatterns presenting biomolecules and signaling molecules - Cai, Chengzhi

• Suh.ppt - Reengineering Adeno-Associated Virus - Suh, Junghae

• cutaneous nanotoxicology.shs - Cutaneous Nanotoxicology - Wilkerson, Michael

• CHIU Centers 07-08-27.pdf - Chiu's NIH Centers at Baylor College of Medicine - Chiu, Wah

• Introduction remark.ppt - Introduction Remarks - Chiu, Wah

• Wah Chiu action plan.ppt - Action Plan - Chiu, Wah

• Blaney.ppt - Dan Duncan Cancer Center - Blaney, Susan

• Aigner HOUSTONTALK807.ppt - NIH Nanomedicine Roadmap - Aigner, Thomas

• Judy CBEN.ppt - NSF Nanotechnology - Judy Raper

• Larry GCNN-LAN-082707 (final).ppt - NCI Nanomedicine Alliance - Nagahara, Larry

• Lee 82707.ppt - NCI Nanomedicine and nano-technology - Lee, Jerry

• Karen.ppt - Recommendations: Leadership and Organization - Ethun, Karen

• Achieving FDA approval for novel new nanomaterials.ppt - Recommendations: Achieving FDA approval for novel nanomaterials - Sevick, Eva M.

• Baylor.ppt - Nanotechnology Center for Mechanics - Michael Sheetz

• Clinical problems for nanotechnology.ppt - Defining the right clinical problems for nanotechnology - Oghalai, John

• Nano discussion.ppt - Challenges for Clinical Applications of Nanotechnology - Eissa, N. Tony

• Cell biology.ppt - Recomendations: Cell Biology and Nanoscience - Sifers, Richard N.

• nanomed-computation.ppt - Recomendations: Computation and Informatics - Baker, Matthew

CryoEM Structure Mining: June 17, 2007

Presentations

• CHIU CryoEM Structure mining 070617.ppt - Introduction to cryoEM - Wah Chiu

CryoEM Training Workshop: June 8, 2007

Presentations

• Cryo_Transfer.mov - Cryo Transfer movie - 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

Introduction to Programming for Scientists Lecture Series: Jun. 12, 2006

Presentations

• lecture1.pdf - Lecture 1 - Simple Datatypes - Steve Ludtke

• lecture2.pdf - Lecture 2 - Lists, Tuples and Dictionaries - Steve Ludtke

• lecture3.pdf - Lecture 3 - if, while, for - Steve Ludtke

• lecture4.pdf - Lecture 4 - Review of homework and File I/O - Steve Ludtke

• pycrust-20060629-1132.py - Examples from review - Steve Ludtke

  • lecture6-examples.ppt - Lecture 6 notes

  • test2.py - Scrabble program from Lecture 6

  • test.py - Box file scaling example from lecture 6

• pycrust-20060706-1134.py - Partial interactive session from lecture 6 - Steve Ludtke

• pycrust-20060710-1112.py - Demo session from lecture 7 - Steve Ludtke

• lecture7-stdlib.pdf - Lecture 7 - Standard Library - Steve Ludtke

• lecture8-numbers.pdf - Lecture 8 - Numbers and CPUs - Steve Ludtke

• lecture9-external.pdf - Lecture 9 - External Packages - Steve Ludtke

• lecture10-eman.pdf - Lecture 10 - EMAN & Chimera - Steve Ludtke

Single Particle Reconstructions and Visualization EMAN Tutorial: Mar. 16 - Mar. 19, 2005

Presentations

• Llorca.ppt - Using EMAN to obtain 3D reconstructions of asymmetric and/or small proteins - Helen Berman

• final.ppt - Robbie Reutzel

• EMAN_workshop_March_05_talk.ppt - Three-dimensional Reconstruction of the PA200-20S Proteasome Complex by Cryo-EM - Joaquin Ortega

• Chiu_EMAN Workshop_05_03_16.pdf - Wah Chiu

• Talk1.pdf - Introduction to EMAN - Steven Ludtke

• Tak1.pt2.pdf - Introduction to EMAN - Pt2 - Steven Ludtke

• Talk2.pdf - Model Bias and CTF Correction - Steven Ludtke

• Demo1.pdf - EMAN Demo - day 1 - Steven Ludtke

• Demo2.pdf - EMAN Demo - day 2 - Steven Ludtke

• workshop-baker.ppt - I have a Structure, What Now? - Matthew Baker

• python.pdf - EMAN - Python programming - Steven Ludtke

• 2005Mar17_computer_driven_microscopy.ppt - JAMES and Mr. T. - Christopher Booth

• 2005-SingleParticleWorkshop-Wen-Jiang.ppt - Icosahedral Reconstruction - Wen Jiang

• EMANworkshop.pdf - Multiscale Structural Visualization with UCSF Chimera - Tom Ferrin

• groel.pdf - Chimera Visualization Tutorial - GroEL - Thomas Goddard

• semliki.pdf - Chimera Demonstration - Semliki Forest Virus - Thomas Goddard

• Wrks_EMAN_Resolution_05.pdf - Resolution Criteria - Pawel Penczek

• Wrks_EMAN_tomoV05.pdf - 3D Reconstruction - Pawel Penczek

Workshop of the Center of Protein Folding Machinery: Dec. 4 - Dec. 5, 2004

Presentations

• Chiu_Dec workshop.ppt - Vision of the Protein Folding Machinery Project - Wah Chiu

• FRYDMAN WORKSHOP 12-04.ppt - Biology and medicine of the chaperoning - Judith Frydman

• J King.ppt - Genetics and Chemistry of protein folding - Jonathan King

• CPF_Talk.ppt - Computational approaches in protein folding - Tanya Raschke (Michael Levitt)

• Nanomedicine-Dec-2004.ppt - Crystallography of chaperoning - Paul Adams

• present.ppt - Single Particle Reconstructions of GroEL, Resolution and Heterogeneity - Steven Ludtke

• ChiuStanfordWorkshop4Dec04.ppt - Modeling the structures of proteins and macromolecular assemblies - Andrej Sali

• Workshop-CPFMdec04.ppt - Single-Molecule Dynamical Approaches for Biological Machines - W. E. Moerner

• Tanja_Kortemme.ppt - Prediction and design of protein-protein interactions - Tanja Kortemme

• kwp.ppt - Simple Models of Protein Folding - Kevin Plaxco

• StanfordFoldingWorkshop-2004b.ppt - Simulations of protein folding and misfolding - Vijay Pande

National Center for Macromolecular Imaging Workshop on Single Particle Reconstructions and Visualization (& EMAN Tutorial): Dec. 11 - Dec. 15, 2002

Presentations

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/07penszak.wmv - 2D Alignment and Measures of Similarity - Pawel Penczek

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/05penszak.wmv - 3D Reconstruction Algorithms and Resolution Measures - Pawel Penczek

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/06ludtke.wmv - CTF Parameterization and Correction - Steve Ludtke

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/08ludtke.wmv - Difficult Reconstruction Cases and EMEN - Steve Ludtke

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/09bakerjiang.wmv - Helixhunter and Foldhunter - Wen Jiang and Matt Baker

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/04chiu.wmv - Image Contrast Theory - Wah Chiu

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/01crowther1.wmv - Image Processing Basics I - Tony Crowther

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/02crowther2.wmv - Image Processing Basics II - Tony Crowther

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/03ludtke.wmv - Intro to EMAN - Steve Ludtke

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/11dougherty.wmv - Scientific Animation - Matt Dougherty

• http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/10abajaj.wmv - Scientific Visualization - Chandrajit Bajaj

Image Processing Workshop - Theory and Practice of Icosahedral Particle Reconstruction: Apr. 9, 2002

Presentations

• lecture.ppt - Lecture - Tony Crowther