• Ws2015

NCMI Workshop on Single Particle Reconstruction, Structural Variability and Modeling

Oct 30 - Nov 2, 2015

We strongly recommend bringing a 3 button (or 2 button+scroll) mouse. While it is possible to survive with a trackpad or one button mouse, there are many things in EMAN and Chimera where having additional mouse buttons is VERY useful.

The official agenda is on the Workshop Page

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

• Ludtke - Workshop Introduction

• EMAN2.12 Tutorial - Part 1 (session starts at 4:20 in video)

• EMAN2.12 Tutorial - Part 2 - 2-D Class averages

• EMAN2.12 Tutorial - Part 3 - Starting your first refinement

• 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

• Baker - Model building tutorial

Tutorial PDFs

• EMAN2-12_Tutorial.pdf

• EMAN2-12_Tutorial2_heterogeneity.pdf

  • Please note that e2refine_split has been improved significantly since 2.12. Suggest an update if using this method.

• Segger Tutorials

• PathwalkerGorgonTutorial.pdf

• ModelOptimizationTutorial.pdf

• ModelValidationTutorial.pdf

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

• Bgal.zip

• ribosome.zip

• segger_workshop_files.zip

• sparx_sorting.tgz

• Data-Sets.zip from Gorgon site

• sparx_ctf.tgz - NEW

• Optimize-tutorial.zip

• Validate-tutorial.zip

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

• Optimize_Results.zip

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

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 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 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