== NCMI Workshops: Cryo EM Image Processing == ''' [[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_125|Cryo-EM Workshop at the National University of Singapore: July 9 - July 13, 2012]] ''' '''Presentations''' * [[attachment:emviz.pdf]] - Map Visualization with Chimera - Tom Goddard * [[attachment:CHIU CryoEM lecture NUS workshop 2012.pdf]] - CryoEM Basics - Wah Chiu * [[attachment:Model_bias.pdf]] - Model Bias- Mini Lecture Quantitative - Steve Ludtke * [[attachment:Particle_Eval.pdf]] - Particle Analysis (mini-lecture) - Steve Ludtke * [[attachment:EMAN2_Intro.pdf]] - EMAN2 Introduction - Steve Ludtke * [[attachment:Single_Particle_Intro.pdf]] - Introduction to Single Particle Analysis - Steve Ludtke * [[attachment:Lu Gan NUS cryo-ET lecture.pdf]] - Cryo-ET Basics - Lu Gan * [[attachment:Slides_for_workshop3_handout_red.pdf]] - Single Particle Tomography slides/handout - Michael Schmid et al * [[attachment:Flagella01-07-10-2012_red.pdf]] - Trypanosome Flagella - Schmid, M, Koyfman AY, Gheiratmand L, Fu CJ, Khant HA, Huang D, He CY, Chiu W * [[attachment:CHIU CryoEM Modeling NUS-reduced.pdf]] - CHIU Modeling Lecture - Wah Chiu ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_97|Structural & Computational Biomedical Informatics and Cryo-EM (UK): June 8 - June 12, 2009]] ''' '''Presentations''' * [[attachment:workflow_tutorial_final.pdf]] - EMAN2 Workflow Tutorial (Revised) - Steve Ludtke * [[attachment:Workshop_1.pdf]] - Introduction to Single Particle Reconsruction and EMAN2 - lecture notes - Steve Ludtke ---- ''' [[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_91|EMAN/Single Particle Tutorial: June 11, 2008]] ''' '''Presentations''' * [[attachment:Talk1.pdf]] - Introduction to Single Particle Reconstruction in EMAN1 - Steve Ludtke * [[attachment:talk2-ctf.pdf]] - Introduction to Fourier Transforms and CTF Correction - Steve Ludtke * [[attachment:Demo1.pdf]] - Demo session containing walkthrough for EMAN1 DVD - Steve Ludtke * [[attachment:ffts.pdf]] - FFT's Part 1 (more detailed lecture) - Steve Ludtke * [[attachment:ffts2.pdf]] - FFT's Part 2 (more detailed lecture) - Steve Ludtke ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_85|Grand challenges for Nanomedicine and Nanobiology: Aug 27, 2007]] ''' '''Presentations''' * [[attachment:ACS poster.ppt||&do=get]] - Single-walled Carbon Nanotubes in the Intact Organism:Near-IR Imaging and Biocompatibility Studies in Drosophila - Beckingham, Kathleen * [[attachment:collaboration.ppt||&do=get]] - Surfaces/nanopatterns presenting biomolecules and signaling molecules - Cai, Chengzhi * [[attachment:Suh.ppt||&do=get]] - Reengineering Adeno-Associated Virus - Suh, Junghae * [[attachment:cutaneous nanotoxicology.shs||&do=get]] - Cutaneous Nanotoxicology - Wilkerson, Michael * [[attachment:CHIU Centers 07-08-27.pdf]] - Chiu's NIH Centers at Baylor College of Medicine - Chiu, Wah * [[attachment:Introduction remark.ppt||&do=get]] - Introduction Remarks - Chiu, Wah * [[attachment:Wah Chiu action plan.ppt||&do=get]] - Action Plan - Chiu, Wah * [[attachment:Blaney.ppt||&do=get]] - Dan Duncan Cancer Center - Blaney, Susan * [[attachment:Aigner HOUSTONTALK807.ppt||&do=get]] - NIH Nanomedicine Roadmap - Aigner, Thomas * [[attachment:Judy CBEN.ppt||&do=get]] - NSF Nanotechnology - Judy Raper * [[attachment:Larry GCNN-LAN-082707 (final).ppt||&do=get]] - NCI Nanomedicine Alliance - Nagahara, Larry * [[attachment:Lee 82707.ppt||&do=get]] - NCI Nanomedicine and nano-technology - Lee, Jerry * [[attachment:Karen.ppt||&do=get]] - Recommendations: Leadership and Organization - Ethun, Karen * [[attachment:Achieving FDA approval for novel new nanomaterials.ppt||&do=get]] - Recommendations: Achieving FDA approval for novel nanomaterials - Sevick, Eva M. * [[attachment:Baylor.ppt||&do=get]] - Nanotechnology Center for Mechanics - Michael Sheetz * [[attachment:Clinical problems for nanotechnology.ppt||&do=get]] - Defining the right clinical problems for nanotechnology - Oghalai, John * [[attachment:Nano discussion.ppt||&do=get]] - Challenges for Clinical Applications of Nanotechnology - Eissa, N. Tony * [[attachment:Cell biology.ppt||&do=get]] - Recomendations: Cell Biology and Nanoscience - Sifers, Richard N. * [[attachment:nanomed-computation.ppt||&do=get]] - Recomendations: Computation and Informatics - Baker, Matthew ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_84|CryoEM Structure Mining: June 17, 2007]] ''' '''Presentations''' * [[attachment:CHIU CryoEM Structure mining 070617.ppt||&do=get]] - Introduction to cryoEM - Wah Chiu ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_83|CryoEM Training Workshop: June 8, 2007]] ''' '''Presentations''' * [[http://blake.bcm.edu/dl/NCMI_training/Cryo_Transfer.mov|Cryo transfer]] - Cruciano, Angela; Rees, Ian * [[attachment:Chiu handout 1 07-06-08.ppt||&do=get]] - Day 1 Lecture- Overview of Cryo EM - Wah Chiu * [[attachment:MDS Alignment.ppt||&do=get]] - MDS alignment - Cruciano, Angela ---- ''' [[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_60|Introduction to Programming for Scientists Lecture Series: Jun. 12, 2006]] ''' '''Presentations''' * [[attachment:lecture1.pdf]] - Lecture 1 - Simple Datatypes - Steve Ludtke * [[attachment:lecture2.pdf]] - Lecture 2 - Lists, Tuples and Dictionaries - Steve Ludtke * [[attachment:lecture3.pdf ]] - Lecture 3 - if, while, for - Steve Ludtke * [[attachment:lecture4.pdf]] - Lecture 4 - Review of homework and File I/O - Steve Ludtke * [[attachment:pycrust-20060629-1132.py||&do=get]] - Examples from review - Steve Ludtke * [[attachment:lecture6-examples.ppt||&do=get]] - Lecture 6 notes * [[attachment:test2.py||&do=get]] - Scrabble program from Lecture 6 * [[attachment:test.py||&do=get]] - Box file scaling example from lecture 6 * [[attachment:pycrust-20060706-1134.py||&do=get]] - Partial interactive session from lecture 6 - Steve Ludtke * [[attachment:pycrust-20060710-1112.py||&do=get]] - Demo session from lecture 7 - Steve Ludtke * [[attachment:lecture7-stdlib.pdf]] - Lecture 7 - Standard Library - Steve Ludtke * [[attachment:lecture8-numbers.pdf]] - Lecture 8 - Numbers and CPUs - Steve Ludtke * [[attachment:lecture9-external.pdf]] - Lecture 9 - External Packages - Steve Ludtke * [[attachment:lecture10-eman.pdf]] - Lecture 10 - EMAN & Chimera - Steve Ludtke ---- ''' [[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_47|Workshop of the Center of Protein Folding Machinery: Dec. 4 - Dec. 5, 2004]] ''' '''Presentations''' * [[attachment:Chiu_Dec workshop.ppt||&do=get]] - Vision of the Protein Folding Machinery Project - Wah Chiu * [[attachment:FRYDMAN WORKSHOP 12-04.ppt ||&do=get]] - Biology and medicine of the chaperoning - Judith Frydman * [[attachment:J King.ppt||&do=get]] - Genetics and Chemistry of protein folding - Jonathan King * [[attachment:CPF_Talk.ppt||&do=get]] - Computational approaches in protein folding - Tanya Raschke (Michael Levitt) * [[attachment:Nanomedicine-Dec-2004.ppt||&do=get]] - Crystallography of chaperoning - Paul Adams * [[attachment:present.ppt||&do=get]] - Single Particle Reconstructions of GroEL, Resolution and Heterogeneity - Steven Ludtke * [[attachment:ChiuStanfordWorkshop4Dec04.ppt||&do=get]] - Modeling the structures of proteins and macromolecular assemblies - Andrej Sali * [[attachment:Workshop-CPFMdec04.ppt||&do=get]] - Single-Molecule Dynamical Approaches for Biological Machines - W. E. Moerner * [[attachment:Tanja_Kortemme.ppt||&do=get]] - Prediction and design of protein-protein interactions - Tanja Kortemme * [[attachment:kwp.ppt||&do=get]] - Simple Models of Protein Folding - Kevin Plaxco * [[attachment:StanfordFoldingWorkshop-2004b.ppt||&do=get]] - Simulations of protein folding and misfolding - Vijay Pande ---- ''' [[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 ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_19|Image Processing Workshop - Theory and Practice of Icosahedral Particle Reconstruction: Apr. 9, 2002]] ''' '''Presentations''' * [[attachment:lecture.ppt||&do=get]] - Lecture - Tony Crowther ----