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| ''' Click above for the Workshop presentations ''' | '''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 |
NCMI Workshops: Cryo EM Data Collection
Click the link below to watch the video
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
EMAN2.12 Tutorial - Part 1 (session starts at 4:20 in video)
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
Tutorial PDFs
EMAN2-12_Tutorial2_heterogeneity.pdf
- Please note that e2refine_split has been improved significantly since 2.12. Suggest an update if using this method.
Tutorial Data You will also need all of the demonstration data, which we will use when going through the tutorials:
Data-Sets.zip from Gorgon site
sparx_ctf.tgz - NEW
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
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
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
CryoEM Workshop: Oct. 17, 2006
Presentations
2006Oct18CryoEMCourseCCDs.ppt - Introduction To Using CCD Cameras In cryo-EM - Booth, Christopher
CHIU Handout CryoEM Rice 06-10-18.ppt - CryoEM Lecture for Biophysics Course and Workshop on Oct 18 2006 - Wah Chiu
Cryo TEM from specimen prep to the microscope_Gatan Presentation_LAM1.pdf - Cryo TEM from specimen prep to the microscope - Linda Melanson
CryoEM_Imaging_NCMI_20061018.pdf - Imaging in Cryo-electron microscopy - Brink, Jaap
Frederik.pdf - CryoEM of supsension - Professor Peter Frederik
Tutorial of TEM for Biological Cryo-Specimens: Oct. 11, 2004
Presentations
EMtutorial.pdf - EM Tutorial (2004) - Wah Chiu
gridClean_Li.ppt - Grid Cleaning - Zongli Li
Tutorial on CryoEM: Oct. 18, 2003
Presentations
EM Tutorial_03_10_18.ppt - Basics of electron microscope - Wah Chiu
EMPresentation_Glen_1018-2003.ppt - Grid for TEM - Glen Decker
ISvitrification2003.ppt - Theory on Cryo-EM Preparation - Irina Serysheva