NCMI Workshops: Cryo EM Modeling

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

Modeling of Cryo-EM map Workshop: Jan 14 - Jan 17, 2010

Presentations

• modeling2010_tao.pdf - Geometric Algorithms for De Novo Modeling - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah

• PDB_Items_for_EM.ppt - PDB Items for EM (EMDB Schema) - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah

• HoustonWorkshopJan2010-v4.ppt - EM Maps and Models in EMDB/PDB - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah

• xray-validation-for-em.ppt - Applied common sense: The why, what and how of validation - Kleywegt, Gerard J.

• Baker-workshop2010.pdf - De Novo Modeling with Cryo-EM Density Maps - Baker, Matthew

• 2010-01-16 NCMI Baylor Workshop 90min Sali.pdf - Integrative structure determination at pseudo-atomic resolution - Andrej Sali

• 2010 Jan Mesoscale CryoEM Workshop.pdf - MESOSCALE MODELING OF MACROMOLECULAR MACHINES - Michael Levitt

• EMdepoInstructions2010.doc - EM Depo Instructions - Lawson, Cathy

• Schulten1.pdf - Molecular Modeling Flexible Fitting 1: Introduction to Molecular Dynamics - Schulten, Klaus

• Schulten2.pdf - Molecular Modeling Flexible Fitting 2: Introduction to Method - Schulten, Klaus

• Schulten3.pdf - Molecular Modeling Flexible Fitting 3: Application to Ribosome - Schulten, Klaus

• EMD5127-3iyd.ppt - Deposition example EMD-5127-PDB-3iyd - Lawson, Cathy

• EMdepoTutorial2010.doc - EM Deposition Tutorial - Lawson, Cathy

• talk-houston_jan10-schroeder.pdf - Structure Refinement at Low Resolution - Schroeder, Gunnar

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

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

Visualization of Large Biomolecular Complexes: Sep. 11 - Sep. 13, 2005

Presentations

• - Multi-Field Biomedical Visualization - Chris Johnson

• EllipsoidMolecules.ppt - Hierarchical Molecular Modelling with Ellipsoids - Nelson Max

• Moreland_AltReps.ppt - Alternative Representations for Biological Complexes - John L. Moreland

• Lawson_2005_vis_workshop.ppt - Visualisation of Large Biomolecular Complexes - Lawson, Cathy

• SanDiego.ppt - Hierarchical Molecular Modelling with Ellipsoids: long version - Nelson Max

• PPInterfaces_FCazals_VLBC.pdf - Revisiting the description of Protein-Protein interfaces - F. Cazals

• - Software Components for Modeling Large Bimolecular Complexes - Michel Sanner

• chimera-sep2005.pdf - Exploring Large Molecular Complexes with UCSF Chimera - Tom Goddard

• MBaker-visworkshop.ppt - Visualization and Analysis of Macromolecular Complexes - Baker, Matthew

• Varshney05.ppt - Molecular Visualization: Advances and Challenges - Varshney, Amitabh

• snoeyink-biomolecvis05.ppt - Geometric algorithms in biomolecular visualization & analysis - Jack Snoeyink

• delano_pymol.ppt - Is PyMOL Ready to Handle Large Biomolecular Complexes? - DeLano, Warren L.

• 2005_09_12_Bajaj_Alg_Talk.pdf - Geometric and Signal 3D Processing and some Visualization - Bajaj, Chandra

• 2005_taylor_bimolecular_v2.ppt - Displaying Two Intimate Surfaces, multiple scalar fields, etc - Russell M. Taylor II, Chris Weigle, Alexandra Bokinsky, David Borland, others.

• vmdvlbc2005.ppt - VMD: Algorithms and Methods for Visualizing Large Biomolecular Complexes - Stone, John

• bio-visualization.ppt - Visualization Wish lists - Vijay Reddy

• NIH-Biovisualization05-Johnson.ppt - Biomedical Visualization and Software Frameworks - Chris Johnson

• Breakout_Implementation.doc - Break out Group Implementation - All

• BreakOut_Algorithms.doc - Break out Group Algorithms - All

• ActionItems.doc - Action Items - All

• Agenda_for_Vis-workshop.doc - Final Final Agenda - All

• 2005VisPresentation.ppt - Molecular Illustration from Atoms to Cells - Goodsell, David S.

• VisWorkshop.ppt - Software Components for Modeling Large Biomolecular Complexes - Sanner, Michel

• Baker, T. Powerpoint.ppt - Challenges in the Visualization, Analysis, and Interpretation of Large Macromolecular Complexes - Tim S. Baker

Workshop on Structural and Computational Proteomics of Biological Complexes: May. 16 - May. 17, 2005

Presentations

• Baylor.ppt - Data Management in the Protein Data Bank - Oscar Llorca

• Structural Biology Workshop-Jacobson.mov - Purification of S. Cerevisiae TFIID for Structural Studies - Raymond Jacobson

• wenselwkshp05my.ppt - Structural Dynamics of Signal-Transducing Membrane Complexes - Theodore Wensel

• CHIU_Workshop Intro_05_05_16.ppt - Worskhop Introduction - Wah Chiu

• emen2.ppt - EMEN2 - A Distributed Object-oriented Electronic Notebook for Data Archival, Sharing and Mining - Steven Ludtke

• CCBC2005.ppt - Modeling Platform for Collaboration - Zheng Li

• tdavisHoustonupload2005.ppt - The Lattice Structure of the Yeast Spindle Pole Body Probed by Fluorescence Resonance Energy Transfer - Trisha Davis

• markley_sesame_dep.ppt - Sesame: a Data Management System for Structural Proteomics - John Markley

• DASH-C2BCworkshop.pdf - Enhancing Data Sharing in Collaborative Research Projects with DASH - Thomas Ferrin

• ChiuWorkshop Houston17May05.pdf - EMEN2 - Modeling the structures of proteins and macromolecular assemblies - Andrej Sali

• baylor.pdf - Computational study of the binding specificities of SH2 and SH3 domains - Wei Wang

• Baylor talk.ppt - Structural Investigations of Herpesvirus Infection. - Frazer Rixon

• Houston2005-1.ppt - Center for Genomic Experimentation and Computation - Orna Resnekov

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

Visualization of Biological Complexes: Oct. 11 - Oct. 12, 2003

Presentations

• Chiu_Visualization_workshop.ppt - Workshop Goals - Wah Chiu

• Sali Assemblies Wah 11Oct03.ppt - Modeling of macromolecular assemblies - Andrej Sali

• Jiang_Baker_sf2003.ppt - Structural Feature Extraction in Intermediate Resolution Macromolecular Assemblies - Matthew Baker

• Goddard-PDB-Viruses-2003.pdf - Data Quality Problems in PDB Virus Models - Tom Goddard (Michael Levitt)

• Bajaj_2003_10_11_BerkeleyWorkshop.pdf - Quantitative Visualization of Static and Dynamic Biological Complexes - Chandrajit Bajaj

• FerrinMultiscale03.pdf - Multiscale Structural Visualization with UCSF Chimera - Thomas Ferrin

• Carazo-NIH-Oct-2003.ppt - Unreveiling new biological knowledge from multiresolution structural proteomics data - Jose-Maria Carazo

• - Illustrating Molecular Assemblies - David Goodsell

• Berman_visualization2.ppt - Protein Data Bank Challenges - Shuchismita Dutta

• Jiang_Baker_sf2003.ppt - Structural Feature Extraction in Intermediate Resolution Macromolecular Assemblies - Wen Jiang

• delano_pymol.ppt - Issues Surrounding the Use of Open-Source PyMOL to Visualize Large Complexes - Warren Delano

• OlsonBerkeley-03-talk.ppt - Advanced User Interfaces - Back to the Future ? - Arthur J. Olson

• Sanner.ppt - Representation, Implementation, and Interaction: Challenges for Macromolecular Assemblies - Michel Sanner

• BioCompVis_2003.ppt - MBT - The Molecular Biology Toolkit - John Moreland

• Dougherty_Visualization workshop.ppt - Visualization activities at NCMI - Matthew Dougherty

• - Building visualization and analysis applications using Molecular Biology Toolkit - Sasha Buzko

• Apostol_Draft.ppt - The Molecular Biology Toolkit - Geometry Engine Capabilities - Apostle Gramada

Workshop on Structural Proteomics of Biological Complexes: Apr. 7 - Apr. 8, 2003

Presentations

• Chiu_Visualization_workshop.ppt - Workshop Goals - Wah Chiu

• Drubin.ppt - Why Studying Large Protein Complexes is Crucial at this Time - David Drubin

• Jack Greenblatt.ppt - Protein Complexes in Transcription - Jack Greenblatt

• - Chromosome Segregation and Kinetochore Structure in Yeast - Peter K. Sorger

• - Protein Complexes in Cell Division in Eggs from Xenopus Laevis - Rebecca Heald

• Yates.ppt - Analysis of Protein Complexes by Mass Spectrometry - John Yates

• Boone.ppt - Synthetic Genetic Array Analysis: Large-Scale Mapping of Genetic Interactions Networks in Yeast - Charlie Boone

• - Mining Relevance from the Mycobacterium Tuberculosis Genome and Structural Database - William Jacobs

• Gerstein.ppt - Computational Proteomics: Prediction of Protein Interactions and Function on a Genome-Scale - Mark Gerstein

• Sali.ppt - Modeling the Structures of Molecular Assemblies by Satisfaction of Spatial Restraints - Andrej Sali

• Downing.ppt - Electron Crystallography: Current State and Prospects - Ken Downing

• Milligan.ppt - The Combined Use of Cryo-Electron Microscopy and X-Ray Crystallography to Understand the Structure and Mechanisms of Molecular Machines - Ron Milligan

• Almo.ppt - Structural Proteomics: Structural Dissection of Protein Machines - Steve Almo

• - Structural Proteomics of Infectious Agents - David Stuart

• Kurosky.ppt - Proteomics in Airway Inflammation - Alex Kurosky

• Buchanan.ppt - New Approaches for High-Throughput Identification and Characterization of Protein Complexes - Michelle Buchanan

• Davis.ppt - Yeast Resource Center - Trisha Davis

• Makowski.ppt - Realistic Goals and Milestones; Resources Needed and Funding Mechanisms - Lee Makowski

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

Presentations

• 07penszak.wmv - 2D Alignment and Measures of Similarity - Pawel Penczek

• 05penszak.wmv - 3D Reconstruction Algorithms and Resolution Measures - Pawel Penczek

• 06ludtke.wmv - CTF Parameterization and Correction - Steve Ludtke

• 08ludtke.wmv - Difficult Reconstruction Cases and EMEN - Steve Ludtke

• 09bakerjiang.wmv - Helixhunter and Foldhunter - Wen Jiang and Matt Baker

• 04chiu.wmv - Image Contrast Theory - Wah Chiu

• 01crowther1.wmv - Image Processing Basics I - Tony Crowther

• 02crowther2.wmv - Image Processing Basics II - Tony Crowther

• 03ludtke.wmv - Intro to EMAN - Steve Ludtke

• 11dougherty.wmv - Scientific Animation - Matt Dougherty

• 10abajaj.wmv - Scientific Visualization - Chandrajit Bajaj