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'''Presentations'''
 * [[attachment:wah-introduction.pdf]] - Introduction to the Workshop and NCMI
 * [[attachment:ludtke-overview.pdf]] - Workshop Overview - Steve Ludtke
 * [[attachment:mcmullanintro.pdf]] - Electron Microscopes & Imaging Artifacts - Greg !McMullan
 * [[attachment:penczek-alignment.pdf]] - 2D Alignment Theory - Pawel Penczek
 * [[attachment:ludtke-minitalks.pdf]] - 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]] - 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

----
=== Additional information and tips about software installation ===
These are not additional downloads, but rather are links which may assist in installing some of the required packages above.

 * Please insure that you meet the specific version requirements above for each software package. Tutorials will be tested only on these specific versions.
 * Mac users - If you are running El Capitan on your Mac (10.11) you will find there are a few bugs specific to this OS version we have not managed to fix yet. It should still be possible to complete the tutorial, but you will encounter a few annoyances.
 * OpenMPI/Pydusa - Most SPARX tasks require MPI to run correctly, and are normally used on clusters. It is possible to install MPI on a single laptop/desktop as well, and requires minimal work or configuration to do so, you will simply be limited to the number of CPUs available on your laptop. Much of the SPARX presentation will be 'demo style' rather than a formal tutorial anyway, so you will not miss too much if you don't get MPI configured. Instructions are available [[http://blake.bcm.edu/emanwiki/EMAN2/Parallel/Mpi|here]].
 * Due to the required computation for most Relion refinements, Sjors plans to run a demo-style session rather than a tutorial. However, if you install Relion, you may be able to experiment with it a bit during the session. This is recommended only for users with Linux on their laptops.
 * Chimera and Phenix have some restrictions on commercial use. If you work for a commercial entity, and your IT group will not install these packages, you will still be able to directly participate in most of the workshop. Phenix will only be used at the very end of day 4 to learn about real-space refinement. Chimera will be used on day 4 for a segmentation tutorial. It is also a useful utility to have available, but should otherwise not be strictly required.
 * Warning - there may be some minor issues with EMAN/SPARX 2.12 on MacOS ElCapitan. If you have not upgraded, you may consider delaying until after the workshop.
 * Installing EMAN2/SPARX:
  * Instructions are here: [[http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall]]
 * Installing Phenix:
  * Go to http://www.phenix-online.org/download/ and click request download instructions.
  * Register (http://www.phenix-online.org/phenix_request/index.cgi) with institutional email address.
  * Then an email with a password for the download will be sent to the registered email address.
  * Use the provided link and password to download the latest official release (for example: Latest official release: 1.10.1-2155 (10-06-2015)).
  * The user should then install the command line operator version for their particular operating system.
  * Unzip the downloaded file (~918MB) and follow the install instructions in the README file (you may need to use > sudo ./install). I would suggest to install in the default directory (usr/local/..).
  * Once you have successfully installed PHENIX, to set up your environment please source the phenix_env file in the phenix installation directory (as stated in the README file).
 * Installing LKH Solver
  * For linux you can download source and compile using the link above
  * For the Mac
   * You can build from source if you have Xcode - or -
   * We are providing a Mac binary [[attachment:lkh]] you can 'chmod a+x lkh' then copy to /usr/local/bin (or another folder in your $PATH)
  * For Windows, there is a binary version available: [[http://www.akira.ruc.dk/~keld/research/LKH/lkh.exe]]		 ''' [[http://blake.bcm.edu/emanwiki/Ws2015|Workshop presentations]] '''

NCMI Workshops: Cryo EM Modeling

Workshop on Single Particle Reconstruction, Structural Variability and Modeling: Oct 30 - Nov 2, 2015

Workshop presentations

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

Presentations

Workshop on Single Particle Reconstruction, Map Interpretation and Visualization: Dec 10 - Dec 13, 2008

Presentations

Workshop on Single Particle Reconstruction and Visualization: Mar. 14, 2007

Presentations

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

Presentations

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

Presentations

Single Particle Reconstructions and Visualization EMAN Tutorial: Mar. 16 - Mar. 19, 2005

Presentations

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

Presentations

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

CryoEMModeling (last edited 2016-06-03 19:28:40 by SnekaRaveendran)