== NCMI Workshops: Cryo EM Data Collection == '''Click the link below to watch the video''' *[[http://blake.bcm.edu/dl/NCMI_training/Vacuum_diagram_movie.mov|Vaccum diagram movie]] ---- ''' [[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_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_64|CryoEM Workshop: Oct. 17, 2006]] ''' '''Presentations''' * [[attachment:2006Oct18CryoEMCourseCCDs.ppt||&do=get]] - Introduction To Using CCD Cameras In cryo-EM - Booth, Christopher * [[attachment:CHIU Handout CryoEM Rice 06-10-18.ppt||&do=get]] - CryoEM Lecture for Biophysics Course and Workshop on Oct 18 2006 - Wah Chiu * [[attachment:Cryo TEM from specimen prep to the microscope_Gatan Presentation_LAM1.pdf]] - Cryo TEM from specimen prep to the microscope - Linda Melanson * [[attachment:CryoEM_Imaging_NCMI_20061018.pdf||&do=get]] - Imaging in Cryo-electron microscopy - Brink, Jaap * [[attachment:Frederik.pdf]] - CryoEM of supsension - Professor Peter Frederik ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_8|Tutorial of TEM for Biological Cryo-Specimens: Oct. 11, 2004]] ''' '''Presentations''' * [[attachment:EMtutorial.pdf||&do=get]] - EM Tutorial (2004) - Wah Chiu * [[attachment:gridClean_Li.ppt ||&do=get]] - Grid Cleaning - Zongli Li ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_43|Tutorial on CryoEM: Oct. 18, 2003]] ''' '''Presentations''' * [[attachment:EM Tutorial_03_10_18.ppt||&do=get]] - Basics of electron microscope - Wah Chiu * [[attachment:EMPresentation_Glen_1018-2003.ppt ||&do=get]] - Grid for TEM - Glen Decker * [[attachment:ISvitrification2003.ppt ||&do=get]] - Theory on Cryo-EM Preparation - Irina Serysheva ----