== NCMI Workshops: Cryo EM Modeling == ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_145|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) * [[attachment:wah-introduction.pdf]] - Introduction to the Workshop and NCMI * [[attachment:ludtke-overview.pdf||&do=get]] - Workshop Overview - Steve Ludtke * [[attachment:mcmullanintro.pdf]] - Electron Microscopes & Imaging Artifacts - Greg !McMullan * [[attachment:penczek-alignment.pdf||&do=get]] - 2D Alignment Theory - Pawel Penczek * [[attachment:ludtke-minitalks.pdf||&do=get]] - CTF, Refinement, other topics - Steve Ludtke * [[attachment:baldwin-orientation.pdf]] - Orientation and Symmetry - Phil Baldwin * [[attachment:scheres-heterogeneity.pdf]] - Methods for Heterogeneity Analysis - Sjors Scheres * [[attachment:mcmullanDetector.pdf]] - Direct Detector Technology - Greg !McMullan * [[attachment:pintilie.pdf]] - Chimera & Segger - Greg Pintilie * [[attachment:baker-model-building.pdf||&do=get]] - Model Building - Matt Baker * [[attachment: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 * [[http://blake.grid.bcm.edu/videos/NCMI_workshop_2015/Ludtke_session_1-Workshop_intro.mp4|Ludtke - Workshop Introduction]] * [[http://blake.grid.bcm.edu/videos/NCMI_workshop_2015/Ludtke_session_2-EMAN2_tutorial_1.mp4|EMAN2.12 Tutorial - Part 1 ]] (session starts at 4:20 in video) * [[http://blake.grid.bcm.edu/videos/NCMI_workshop_2015/Ludtke_session_3-class_eval.mp4|EMAN2.12 Tutorial - Part 2 - 2-D Class averages]] * [[http://blake.grid.bcm.edu/videos/NCMI_workshop_2015/Ludtke_session_4-e2refine_easy.mp4|EMAN2.12 Tutorial - Part 3 - Starting your first refinement]] * [[http://blake.grid.bcm.edu/videos/NCMI_workshop_2015/Ludtke_session_5-e2refine_easy_results.mp4|EMAN2.12 Tutorial - Part 4 - Looking at the results of the first refinement]] * [[http://blake.grid.bcm.edu/videos/NCMI_workshop_2015/Ludtke_session_6-heterogeneity.mp4|Compositional and conformational variability in EMAN2.12 - Part 1]] * [[http://blake.grid.bcm.edu/videos/NCMI_workshop_2015/Ludtke_session_7-heterogeneity_2.mp4|Compositional and conformational variability in EMAN2.12 - Part 2]] * [[http://blake.grid.bcm.edu/videos/NCMI_workshop_2015/Baker_modeling_tutorial.mp4|Baker - Model building tutorial]] '''Tutorial PDFs''' * [[attachment:EMAN2-12_Tutorial.pdf||&do=get]] * [[attachment:EMAN2-12_Tutorial2_heterogeneity.pdf||&do=get]] * Please note that e2refine_split has been improved significantly since 2.12. Suggest an update if using this method. * [[http://ncmi.bcm.edu/ncmi/software/segger/docs|Segger Tutorials]] * [[attachment:PathwalkerGorgonTutorial.pdf||&do=get]] * [[attachment:ModelOptimizationTutorial.pdf||&do=get]] * [[attachment:ModelValidationTutorial.pdf||&do=get]] '''Tutorial Data''' You will also need all of the demonstration data, which we will use when going through the tutorials: * [[attachment:Bgal.zip||&do=get]] * [[attachment:ribosome.zip||&do=get]] * [[attachment:segger_workshop_files.zip||&do=get]] * [[attachment:sparx_sorting.tgz||&do=get]] * Data-Sets.zip from [[https://github.com/GorgonCryoEM/Gorgon/releases/tag/workshop-2015|Gorgon site]] * [[attachment:sparx_ctf.tgz||&do=get]] - NEW * [[attachment:Optimize-tutorial.zip||&do=get]] * [[attachment:Validate-tutorial.zip||&do=get]] '''Completed Tutorial Projects (large files)''' * [[attachment:Bgal-completed-tutorial.zip||&do=get]] Result of EMAN high res tutorial (warning, 6 GB download) * [[attachment:ribosome_Relion.zip||&do=get]] Result of Relion tutorial * [[attachment:Optimize_Results.zip||&do=get]] '''Software used at the workshop:''' * [[http://ncmi.bcm.edu/ncmi/software/counter_222/software_133|EMAN/SPARX 2.12]] (or snapshot version released after Oct. 19, 2015) - (day 1 - 2) Required. Do not use an older version. * [[http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Download_%26_install|Relion 1.4]] (optional, day 2-3) - The Relion session will largely be a demo. See comments below. * [[https://www.cgl.ucsf.edu/chimera/download.html#daily|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. * [[https://github.com/GorgonCryoEM/Gorgon/releases/tag/workshop-2015|Gorgon]] - Gorgon Tutorial (day 4) Please install the appropriate binary AND Data-Sets.zip * [[http://www.phenix-online.org/download/|Phenix]] - (end of day 4) real-space refinement of models * [[http://www.akira.ruc.dk/~keld/research/LKH/|LKH Solver]] - (day 4 - pathwalker), required only for the pathwalker tutorial, see below * [[http://www.open-mpi.org/|OpenMPI]] and [[http://ncmi.bcm.edu/ncmi/software/counter_222/software_121|PyDusa]] (day 2-3) SPARX tutorial may also largely be a demo, see below ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_108|Modeling of Cryo-EM map Workshop: Jan 14 - Jan 17, 2010]] ''' '''Presentations''' * [[attachment:modeling2010_tao.pdf]] - Geometric Algorithms for De Novo Modeling - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah * [[attachment:PDB_Items_for_EM.ppt||&do=get]] - PDB Items for EM (EMDB Schema) - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah * [[attachment:HoustonWorkshopJan2010-v4.ppt||&do=get]] - EM Maps and Models in EMDB/PDB - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah * [[attachment:xray-validation-for-em.ppt||&do=get]] - Applied common sense: The why, what and how of validation - Kleywegt, Gerard J. * [[attachment:Baker-workshop2010.pdf]] - De Novo Modeling with Cryo-EM Density Maps - Baker, Matthew * [[attachment:2010-01-16 NCMI Baylor Workshop 90min Sali.pdf]] - Integrative structure determination at pseudo-atomic resolution - Andrej Sali * [[attachment:2010 Jan Mesoscale CryoEM Workshop.pdf||&do=get]] - MESOSCALE MODELING OF MACROMOLECULAR MACHINES - Michael Levitt * [[attachment:EMdepoInstructions2010.doc||&do=get]] - EM Depo Instructions - Lawson, Cathy * [[attachment:Schulten1.pdf]] - Molecular Modeling Flexible Fitting 1: Introduction to Molecular Dynamics - Schulten, Klaus * [[attachment:Schulten2.pdf]] - Molecular Modeling Flexible Fitting 2: Introduction to Method - Schulten, Klaus * [[attachment:Schulten3.pdf]] - Molecular Modeling Flexible Fitting 3: Application to Ribosome - Schulten, Klaus * [[attachment:EMD5127-3iyd.ppt||&do=get]] - Deposition example EMD-5127-PDB-3iyd - Lawson, Cathy * [[attachment:EMdepoTutorial2010.doc||&do=get]] - EM Deposition Tutorial - Lawson, Cathy * [[attachment:talk-houston_jan10-schroeder.pdf]] - Structure Refinement at Low Resolution - Schroeder, Gunnar ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_91|Workshop on Single Particle Reconstruction, Map Interpretation and Visualization: Dec 10 - Dec 13, 2008]] ''' '''Presentations''' * [[attachment:Ludtke_1.pdf]] - Introduction to Single Particle Reconsruction and EMAN2 - Steve Ludtke * [[attachment:workflow_tutorial.pdf]] - EMAN2 Workflow Tutorial - David Woolford * [[attachment:Python_1.pdf]] - Introduction to Python - Steve Ludtke * [[attachment:berman-NCMI-dec08.ppt||&do=get]] - What the Protein Data Bank teaches us about structural biology - Berman, Helen M. * [[attachment:Wrks_EMAN2_08.pdf]] - Introduction - Penczek, Pawel * [[attachment:2008-EMAN-Wen-Jiang.pdf]] - Near-atomic resolution 3-D reconstruction of viruses - Jiang, Wen * [[attachment:2008-12-11 NCMI Baylor Workshop 60min.pdf]] - Integrating Diverse Data for Structure Determination of Macromolecular Assemblies - Andrej Sali ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_66|Workshop on Single Particle Reconstruction and Visualization: Mar. 14, 2007]] ''' '''Presentations''' * [[attachment:houston_march07.ppt||&do=get]] - EMdep: Deposition EM maps - Kim Henrick * [[attachment:Chiu_EMAN Contrast theory_07_03-15.pdf]] - Image Contrast Theory - Wah Chiu * [[attachment:2007-EMAN-Workshop-Wen-Jiang.pdf]] - Icosahedral Reconstruction - Jiang, Wen * [[attachment:EMANworkshop-Ferrin.pdf||&do=get]] - Visualization tools for complex biological structures - Tom Ferrin * [[attachment:chimera-eman-2007.pdf]] - Chimera Tutorial - Tom Goddard * [[attachment:ianrees_emen2_mar8.pdf]] - EMEN2: An Extensible, Collaborative, Electronic Lab Notebook - Rees, Ian * [[attachment:EMAN-workshop07-AIRS.ppt||&do=get]] - VIsualizing and Analyzing CryoEM Density Maps with AIRS - Matthew Baker * [[attachment:EMAN_Wkshp_MFS_Handout.ppt||&do=get]] - Aligning and Averaging 3-D Subvolumes from Electron Cryo-Tomograms - Schmid, Michael * [[attachment:Fourier Transforms.ppt||&do=get]] - Fourier Transforms, Filtering and Convolution - Marsh, Mike * [[attachment:updated_Wrks_EMAN_07.pdf||&do=get]] - updated Image similariry measures and such - Pawel A. Penczek * [[attachment:PmvVision.pdf]] - A Brief Introduction to PMV-VIsion - Zhao, Yong; Sanner, Michel * [[attachment:EMAN_CM_Modeller.ppt||&do=get]] - Introduction to comparative modeling with MODELLER (final version) - Webb, Ben and Topf, Maya * [[attachment:EMAN_Modeller_hands_on.ppt||&do=get]] - MODELLER hands-on session (final version) - Webb, Ben and Topf, Maya * [[attachment:EMANDemo1.pdf]] - EMAN Practical Session Slides - Ludtke, Steven * [[attachment:python_intro.pdf]] - Introduction to Python - Ludtke, Steven * [[attachment:talk1-intro.pdf]] - Workshop Welcome and Single Particle Reconstruction Overview - Ludtke, Steven * [[attachment:talk2-ctf.pdf]] - CTF Correction, Resolution Measurement & Model Bias - Ludtke, Steven ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_52|Visualization of Large Biomolecular Complexes: Sep. 11 - Sep. 13, 2005]] ''' '''Presentations''' * [[attachment:]] - Multi-Field Biomedical Visualization - Chris Johnson * [[attachment:EllipsoidMolecules.ppt||&do=get]] - Hierarchical Molecular Modelling with Ellipsoids - Nelson Max * [[attachment:Moreland_AltReps.ppt||&do=get]] - Alternative Representations for Biological Complexes - John L. Moreland * [[attachment:Lawson_2005_vis_workshop.ppt||&do=get]] - Visualisation of Large Biomolecular Complexes - Lawson, Cathy * [[attachment:SanDiego.ppt||&do=get]] - Hierarchical Molecular Modelling with Ellipsoids: long version - Nelson Max * [[attachment:PPInterfaces_FCazals_VLBC.pdf||&do=get]] - Revisiting the description of Protein-Protein interfaces - F. Cazals * [[attachment:]] - Software Components for Modeling Large Bimolecular Complexes - Michel Sanner * [[attachment:chimera-sep2005.pdf||&do=get]] - Exploring Large Molecular Complexes with UCSF Chimera - Tom Goddard * [[attachment:MBaker-visworkshop.ppt||&do=get]] - Visualization and Analysis of Macromolecular Complexes - Baker, Matthew * [[attachment:Varshney05.ppt||&do=get]] - Molecular Visualization: Advances and Challenges - Varshney, Amitabh * [[attachment:snoeyink-biomolecvis05.ppt||&do=get]] - Geometric algorithms in biomolecular visualization & analysis - Jack Snoeyink * [[attachment:delano_pymol.ppt||&do=get]] - Is PyMOL Ready to Handle Large Biomolecular Complexes? - DeLano, Warren L. * [[attachment:2005_09_12_Bajaj_Alg_Talk.pdf]] - Geometric and Signal 3D Processing and some Visualization - Bajaj, Chandra * [[attachment:2005_taylor_biomolecular_v2.ppt||&do=get]] - Displaying Two Intimate Surfaces, multiple scalar fields, etc - Russell M. Taylor II, Chris Weigle, Alexandra Bokinsky, David Borland, others. * [[attachment:vmdvlbc2005.ppt||&do=get]] - VMD: Algorithms and Methods for Visualizing Large Biomolecular Complexes - Stone, John * [[attachment:bio-visualization.ppt||&do=get]] - Visualization Wish lists - Vijay Reddy * [[attachment:NIH-Biovisualization05-Johnson.ppt||&do=get]] - Biomedical Visualization and Software Frameworks - Chris Johnson * [[attachment:Breakout_Implementation.doc||&do=get]] - Break out Group Implementation - All * [[attachment:BreakOut_Algorithms.doc||&do=get]] - Break out Group Algorithms - All * [[attachment:ActionItems.doc||&do=get]] - Action Items - All * [[attachment:Agenda_for_Vis-workshop.doc||&do=get]] - Final Final Agenda - All * [[attachment:2005VisPresentation.ppt||&do=get]] - Molecular Illustration from Atoms to Cells - Goodsell, David S. * [[attachment:VisWorkshop.ppt||&do=get]] - Software Components for Modeling Large Biomolecular Complexes - Sanner, Michel * [[attachment:Baker, T. Powerpoint.ppt||&do=get]] - Challenges in the Visualization, Analysis, and Interpretation of Large Macromolecular Complexes - Tim S. Baker ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_49|Workshop on Structural and Computational Proteomics of Biological Complexes: May. 16 - May. 17, 2005]] ''' '''Presentations''' * [[attachment:Baylor.ppt||&do=get]] - Data Management in the Protein Data Bank - Oscar Llorca * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/Structural_Biology_Workshop-Jacobson.mov|Structural Biology Workshop-Jacobson.mov]] - Purification of S. Cerevisiae TFIID for Structural Studies - Raymond Jacobson * [[attachment:wenselwkshp05my.ppt||&do=get]] - Structural Dynamics of Signal-Transducing Membrane Complexes - Theodore Wensel * [[attachment:CHIU_Workshop Intro_05_05_16.ppt||&do=get]] - Worskhop Introduction - Wah Chiu * [[attachment:emen2.ppt||&do=get]] - EMEN2 - A Distributed Object-oriented Electronic Notebook for Data Archival, Sharing and Mining - Steven Ludtke * [[attachment:CCBC2005.ppt||&do=get]] - Modeling Platform for Collaboration - Zheng Li * [[attachment:tdavisHoustonupload2005.ppt||&do=get]] - The Lattice Structure of the Yeast Spindle Pole Body Probed by Fluorescence Resonance Energy Transfer - Trisha Davis * [[attachment:markley_sesame_dep.ppt||&do=get]] - Sesame: a Data Management System for Structural Proteomics - John Markley * [[attachment:DASH-C2BCworkshop.pdf||&do=get]] - Enhancing Data Sharing in Collaborative Research Projects with DASH - Thomas Ferrin * [[attachment:ChiuWorkshop Houston17May05.pdf||&do=get]] - EMEN2 - Modeling the structures of proteins and macromolecular assemblies - Andrej Sali * [[attachment:baylor.pdf||&do=get]] - Computational study of the binding specificities of SH2 and SH3 domains - Wei Wang * [[attachment:Baylor talk.ppt||&do=get]] - Structural Investigations of Herpesvirus Infection. - Frazer Rixon * [[attachment:Houston2005-1.ppt||&do=get]] - Center for Genomic Experimentation and Computation - Orna Resnekov ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_7|Single Particle Reconstructions and Visualization EMAN Tutorial: Mar. 16 - Mar. 19, 2005]] ''' '''Presentations''' * [[attachment:Llorca.ppt||&do=get]] - Using EMAN to obtain 3D reconstructions of asymmetric and/or small proteins - Helen Berman * [[attachment:final.ppt ||&do=get]] - Robbie Reutzel * [[attachment:EMAN_workshop_March_05_talk.ppt||&do=get]] - Three-dimensional Reconstruction of the PA200-20S Proteasome Complex by Cryo-EM - Joaquin Ortega * [[attachment:Chiu_EMAN Workshop_05_03_16.pdf||&do=get]] - Wah Chiu * [[attachment:Talk1.pdf||&do=get]] - Introduction to EMAN - Steven Ludtke * [[attachment:Tak1.pt2.pdf||&do=get]] - Introduction to EMAN - Pt2 - Steven Ludtke * [[attachment:Talk2.pdf||&do=get]] - Model Bias and CTF Correction - Steven Ludtke * [[attachment:Demo1.pdf||&do=get]] - EMAN Demo - day 1 - Steven Ludtke * [[attachment:Demo2.pdf||&do=get]] - EMAN Demo - day 2 - Steven Ludtke * [[attachment:workshop-baker.ppt||&do=get]] - I have a Structure, What Now? - Matthew Baker * [[attachment:python.pdf||&do=get]] - EMAN - Python programming - Steven Ludtke * [[attachment:2005Mar17_computer_driven_microscopy.ppt||&do=get]] - JAMES and Mr. T. - Christopher Booth * [[attachment:2005-SingleParticleWorkshop-Wen-Jiang.ppt||&do=get]] - Icosahedral Reconstruction - Wen Jiang * [[attachment:EMANworkshop.pdf||&do=get]] - Multiscale Structural Visualization with UCSF Chimera - Tom Ferrin * [[attachment:groel.pdf||&do=get]] - Chimera Visualization Tutorial - GroEL - Thomas Goddard * [[attachment:semliki.pdf||&do=get]] - Chimera Demonstration - Semliki Forest Virus - Thomas Goddard * [[attachment:Wrks_EMAN_Resolution_05.pdf||&do=get]] - Resolution Criteria - Pawel Penczek * [[attachment:Wrks_EMAN_tomoV05.pdf||&do=get]] - 3D Reconstruction - Pawel Penczek ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_42|Visualization of Biological Complexes: Oct. 11 - Oct. 12, 2003]] ''' '''Presentations''' * [[attachment:Chiu_Visualization_workshop.ppt||&do=get]] - Workshop Goals - Wah Chiu * [[attachment:Sali Assemblies Wah 11Oct03.ppt ||&do=get]] - Modeling of macromolecular assemblies - Andrej Sali * [[attachment:Jiang_Baker_sf2003.ppt||&do=get]] - Structural Feature Extraction in Intermediate Resolution Macromolecular Assemblies - Matthew Baker * [[attachment:Goddard-PDB-Viruses-2003.pdf||&do=get]] - Data Quality Problems in PDB Virus Models - Tom Goddard (Michael Levitt) * [[attachment:Bajaj_2003_10_11_BerkeleyWorkshop.pdf||&do=get]] - Quantitative Visualization of Static and Dynamic Biological Complexes - Chandrajit Bajaj * [[attachment:FerrinMultiscale03.pdf||&do=get]] - Multiscale Structural Visualization with UCSF Chimera - Thomas Ferrin * [[attachment:Carazo-NIH-Oct-2003.ppt||&do=get]] - Unreveiling new biological knowledge from multiresolution structural proteomics data - Jose-Maria Carazo * [[attachment:||&do=get]] - Illustrating Molecular Assemblies - David Goodsell * [[attachment:Berman_visualization2.ppt||&do=get]] - Protein Data Bank Challenges - Shuchismita Dutta * [[attachment:Jiang_Baker_sf2003.ppt||&do=get]] - Structural Feature Extraction in Intermediate Resolution Macromolecular Assemblies - Wen Jiang * [[attachment:delano_pymol.ppt||&do=get]] - Issues Surrounding the Use of Open-Source PyMOL to Visualize Large Complexes - Warren Delano * [[attachment:OlsonBerkeley-03-talk.ppt||&do=get]] - Advanced User Interfaces - Back to the Future ? - Arthur J. Olson * [[attachment:Sanner.ppt||&do=get]] - Representation, Implementation, and Interaction: Challenges for Macromolecular Assemblies - Michel Sanner * [[attachment:BioCompVis_2003.ppt||&do=get]] - MBT - The Molecular Biology Toolkit - John Moreland * [[attachment:Dougherty_Visualization workshop.ppt||&do=get]] - Visualization activities at NCMI - Matthew Dougherty * [[attachment:||&do=get]] - Building visualization and analysis applications using Molecular Biology Toolkit - Sasha Buzko * [[attachment:Apostol_Draft.ppt||&do=get]] - The Molecular Biology Toolkit - Geometry Engine Capabilities - Apostle Gramada ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_37|Workshop on Structural Proteomics of Biological Complexes: Apr. 7 - Apr. 8, 2003]] ''' '''Presentations''' * [[attachment:Chiu_Visualization_workshop.ppt||&do=get]] - Workshop Goals - Wah Chiu * [[attachment:Drubin.ppt ||&do=get]] - Why Studying Large Protein Complexes is Crucial at this Time - David Drubin * [[attachment:Jack Greenblatt.ppt||&do=get]] - Protein Complexes in Transcription - Jack Greenblatt * [[attachment:||&do=get]] - Chromosome Segregation and Kinetochore Structure in Yeast - Peter K. Sorger * [[attachment:||&do=get]] - Protein Complexes in Cell Division in Eggs from Xenopus Laevis - Rebecca Heald * [[attachment:Yates.ppt||&do=get]] - Analysis of Protein Complexes by Mass Spectrometry - John Yates * [[attachment:Boone.ppt||&do=get]] - Synthetic Genetic Array Analysis: Large-Scale Mapping of Genetic Interactions Networks in Yeast - Charlie Boone * [[attachment:||&do=get]] - Mining Relevance from the Mycobacterium Tuberculosis Genome and Structural Database - William Jacobs * [[attachment:Gerstein.ppt||&do=get]] - Computational Proteomics: Prediction of Protein Interactions and Function on a Genome-Scale - Mark Gerstein * [[attachment:Sali.ppt||&do=get]] - Modeling the Structures of Molecular Assemblies by Satisfaction of Spatial Restraints - Andrej Sali * [[attachment:Downing.ppt||&do=get]] - Electron Crystallography: Current State and Prospects - Ken Downing * [[attachment:Milligan.ppt||&do=get]] - The Combined Use of Cryo-Electron Microscopy and X-Ray Crystallography to Understand the Structure and Mechanisms of Molecular Machines - Ron Milligan * [[attachment:Almo.ppt||&do=get]] - Structural Proteomics: Structural Dissection of Protein Machines - Steve Almo * [[attachment:||&do=get]] - Structural Proteomics of Infectious Agents - David Stuart * [[attachment:Kurosky.ppt||&do=get]] - Proteomics in Airway Inflammation - Alex Kurosky * [[attachment:Buchanan.ppt||&do=get]] - New Approaches for High-Throughput Identification and Characterization of Protein Complexes - Michelle Buchanan * [[attachment:Davis.ppt||&do=get]] - Yeast Resource Center - Trisha Davis * [[attachment:Makowski.ppt||&do=get]] - Realistic Goals and Milestones; Resources Needed and Funding Mechanisms - Lee Makowski ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_19|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|07penszak.wmv]] - 2D Alignment and Measures of Similarity - Pawel Penczek * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/05penszak.wmv|05penszak.wmv]] - 3D Reconstruction Algorithms and Resolution Measures - Pawel Penczek * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/06ludtke.wmv|06ludtke.wmv]] - CTF Parameterization and Correction - Steve Ludtke * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/08ludtke.wmv|08ludtke.wmv]] - Difficult Reconstruction Cases and EMEN - Steve Ludtke * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/09bakerjiang.wmv|09bakerjiang.wmv]] - Helixhunter and Foldhunter - Wen Jiang and Matt Baker * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/04chiu.wmv|04chiu.wmv]] - Image Contrast Theory - Wah Chiu * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/01crowther1.wmv|01crowther1.wmv]] - Image Processing Basics I - Tony Crowther * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/02crowther2.wmv|02crowther2.wmv]] - Image Processing Basics II - Tony Crowther * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/03ludtke.wmv|03ludtke.wmv]] - Intro to EMAN - Steve Ludtke * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/11dougherty.wmv|11dougherty.wmv]] - Scientific Animation - Matt Dougherty * [[http://blake.bcm.edu/videos/CryoEM_training/cryoEM_Image_Processing/10abajaj.wmv|10abajaj.wmv]] - Scientific Visualization - Chandrajit Bajaj ----