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'''Presentations'''
'''Presentation notes from the Workshop''' (some of these have not been uploaded yet)
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 * [[attachment:ludtke-overview.pdf]] - Workshop Overview - Steve Ludtke  * [[attachment:ludtke-overview.pdf||&do=get]] - Workshop Overview - Steve Ludtke
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 * [[attachment:penczek-alignment.pdf]] - 2D Alignment Theory - Pawel Penczek
 * [[attachment:ludtke-minitalks.pdf]] - CTF, Refinement, other topics - Steve Ludtke		  * [[attachment:penczek-alignment.pdf||&do=get]] - 2D Alignment Theory - Pawel Penczek
 * [[attachment:ludtke-minitalks.pdf||&do=get]] - CTF, Refinement, other topics - Steve Ludtke
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 * [[attachment:baker-model-building.pdf]] - Model Building - Matt Baker  * [[attachment:baker-model-building.pdf||&do=get]] - Model Building - Matt Baker
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----
=== 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]]
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 * [[attachment:Talk2-ctf.pdf]] - Introduction to Fourier Transforms and CTF Correction - Steve Ludtke  * [[attachment:talk2-ctf.pdf]] - Introduction to Fourier Transforms and CTF Correction - Steve Ludtke
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 * [[attachment:fits.pdf]] - FFT's Part 1 (more detailed lecture) - Steve Ludtke  * [[attachment:ffts.pdf]] - FFT's Part 1 (more detailed lecture) - Steve Ludtke
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 * [[attachment:Cryo_Transfer.mov||&do=get]] - Cryo Transfer movie - Cruciano, Angela; Rees, Ian  * [[http://blake.bcm.edu/dl/NCMI_training/Cryo_Transfer.mov|Cryo transfer]] - Cruciano, Angela; Rees, Ian
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 * [[attachment:07penszak.wmv||&do=get]] - 2D Alignment and Measures of Similarity - Pawel Penczek
 * [[attachment:05penszak.wmv||&do=get]] - 3D Reconstruction Algorithms and Resolution Measures - Pawel Penczek
 * [[attachment:06ludtke.wmv||&do=get]] - CTF Parameterization and Correction - Steve Ludtke
 * [[attachment:08ludtke.wmv||&do=get]] - Difficult Reconstruction Cases and EMEN - Steve Ludtke
 * [[attachment:09bakerjiang.wmv||&do=get]] - Helixhunter and Foldhunter - Wen Jiang and Matt Baker
 * [[attachment:04chiu.wmv||&do=get]] - Image Contrast Theory - Wah Chiu
 * [[attachment:01crowther1.wmv||&do=get]] - Image Processing Basics I - Tony Crowther
 * [[attachment:02crowther2.wmv||&do=get]] - Image Processing Basics II - Tony Crowther
 * [[attachment:03ludtke.wmv||&do=get]] - Intro to EMAN - Steve Ludtke
 * [[attachment:11dougherty.wmv||&do=get]] - Scientific Animation - Matt Dougherty
 * [[attachment:10abajaj.wmv||&do=get]] - Scientific Visualization - Chandrajit Bajaj		  * [[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
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 * [[attachment: lecture.ppt||&do=get]] - Lecture - Tony Crowther

----		  * [[attachment:lecture.ppt||&do=get]] - Lecture - Tony Crowther

----

NCMI Workshops: Cryo EM Image Processing

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)

Video of selected sessions Our primary video recording mechanism failed to record audio, so we unfortunately have only the EMAN and Modeling tutorials recorded

Tutorial PDFs

Tutorial Data You will also need all of the demonstration data, which we will use when going through the tutorials:

Completed Tutorial Projects (large files)

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

Cryo-EM Workshop at the National University of Singapore: July 9 - July 13, 2012

Presentations

Structural & Computational Biomedical Informatics and Cryo-EM (UK): June 8 - June 12, 2009

Presentations

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

Presentations

EMAN/Single Particle Tutorial: June 11, 2008

Presentations

  • Talk1.pdf - Introduction to Single Particle Reconstruction in EMAN1 - Steve Ludtke

  • talk2-ctf.pdf - Introduction to Fourier Transforms and CTF Correction - Steve Ludtke

  • Demo1.pdf - Demo session containing walkthrough for EMAN1 DVD - Steve Ludtke

  • ffts.pdf - FFT's Part 1 (more detailed lecture) - Steve Ludtke

  • ffts2.pdf - FFT's Part 2 (more detailed lecture) - Steve Ludtke

Grand challenges for Nanomedicine and Nanobiology: Aug 27, 2007

Presentations

CryoEM Structure Mining: June 17, 2007

Presentations

CryoEM Training Workshop: June 8, 2007

Presentations

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

Presentations

Introduction to Programming for Scientists Lecture Series: Jun. 12, 2006

Presentations

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

Presentations

Workshop of the Center of Protein Folding Machinery: Dec. 4 - Dec. 5, 2004

Presentations

National Center for Macromolecular Imaging Workshop on Single Particle Reconstructions and Visualization (& EMAN Tutorial): Dec. 11 - Dec. 15, 2002

Presentations

Image Processing Workshop - Theory and Practice of Icosahedral Particle Reconstruction: Apr. 9, 2002

Presentations

CryoEMImageProcessing (last edited 2016-06-03 19:30:54 by SnekaRaveendran)