NCMI Workshops: Cryo EM Image Processing
Presentations
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
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
Cryo-EM Workshop at the National University of Singapore: July 9 - July 13, 2012
Presentations
emviz.pdf - Map Visualization with Chimera - Tom Goddard
CHIU CryoEM lecture NUS workshop 2012.pdf - CryoEM Basics - Wah Chiu
Model_bias.pdf - Model Bias- Mini Lecture Quantitative - Steve Ludtke
Particle_Eval.pdf - Particle Analysis (mini-lecture) - Steve Ludtke
EMAN2_Intro.pdf - EMAN2 Introduction - Steve Ludtke
Single_Particle_Intro.pdf - Introduction to Single Particle Analysis - Steve Ludtke
Lu Gan NUS cryo-ET lecture.pdf - Cryo-ET Basics - Lu Gan
Slides_for_workshop3_handout_red.pdf - Single Particle Tomography slides/handout - Michael Schmid et al
Flagella01-07-10-2012_red.pdf - Trypanosome Flagella - Schmid, M, Koyfman AY, Gheiratmand L, Fu CJ, Khant HA, Huang D, He CY, Chiu W
CHIU CryoEM Modeling NUS-reduced.pdf - CHIU Modeling Lecture - Wah Chiu
Structural & Computational Biomedical Informatics and Cryo-EM (UK): June 8 - June 12, 2009
Presentations
workflow_tutorial_final.pdf - EMAN2 Workflow Tutorial (Revised) - Steve Ludtke
Workshop_1.pdf - Introduction to Single Particle Reconsruction and EMAN2 - lecture notes - Steve Ludtke
Presentations
Ludtke_1.pdf - Introduction to Single Particle Reconsruction and EMAN2 - Steve Ludtke
workflow_tutorial.pdf - EMAN2 Workflow Tutorial - David Woolford
Python_1.pdf - Introduction to Python - Steve Ludtke
berman-NCMI-dec08.ppt - What the Protein Data Bank teaches us about structural biology - Berman, Helen M.
Wrks_EMAN2_08.pdf - Introduction - Penczek, Pawel
2008-EMAN-Wen-Jiang.pdf - Near-atomic resolution 3-D reconstruction of viruses - Jiang, Wen
2008-12-11 NCMI Baylor Workshop 60min.pdf - Integrating Diverse Data for Structure Determination of Macromolecular Assemblies - Andrej Sali
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
fits.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
ACS poster.ppt - Single-walled Carbon Nanotubes in the Intact Organism:Near-IR Imaging and Biocompatibility Studies in Drosophila - Beckingham, Kathleen
collaboration.ppt - Surfaces/nanopatterns presenting biomolecules and signaling molecules - Cai, Chengzhi
Suh.ppt - Reengineering Adeno-Associated Virus - Suh, Junghae
cutaneous nanotoxicology.shs - Cutaneous Nanotoxicology - Wilkerson, Michael
CHIU Centers 07-08-27.pdf - Chiu's NIH Centers at Baylor College of Medicine - Chiu, Wah
Introduction remark.ppt - Introduction Remarks - Chiu, Wah
Wah Chiu action plan.ppt - Action Plan - Chiu, Wah
Blaney.ppt - Dan Duncan Cancer Center - Blaney, Susan
Aigner HOUSTONTALK807.ppt - NIH Nanomedicine Roadmap - Aigner, Thomas
Judy CBEN.ppt - NSF Nanotechnology - Judy Raper
Larry GCNN-LAN-082707 (final).ppt - NCI Nanomedicine Alliance - Nagahara, Larry
Lee 82707.ppt - NCI Nanomedicine and nano-technology - Lee, Jerry
Karen.ppt - Recommendations: Leadership and Organization - Ethun, Karen
Achieving FDA approval for novel new nanomaterials.ppt - Recommendations: Achieving FDA approval for novel nanomaterials - Sevick, Eva M.
Baylor.ppt - Nanotechnology Center for Mechanics - Michael Sheetz
Clinical problems for nanotechnology.ppt - Defining the right clinical problems for nanotechnology - Oghalai, John
Nano discussion.ppt - Challenges for Clinical Applications of Nanotechnology - Eissa, N. Tony
Cell biology.ppt - Recomendations: Cell Biology and Nanoscience - Sifers, Richard N.
nanomed-computation.ppt - Recomendations: Computation and Informatics - Baker, Matthew
CryoEM Structure Mining: June 17, 2007
Presentations
CHIU CryoEM Structure mining 070617.ppt - Introduction to cryoEM - Wah Chiu
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
Introduction to Programming for Scientists Lecture Series: Jun. 12, 2006
Presentations
lecture1.pdf - Lecture 1 - Simple Datatypes - Steve Ludtke
lecture2.pdf - Lecture 2 - Lists, Tuples and Dictionaries - Steve Ludtke
lecture3.pdf - Lecture 3 - if, while, for - Steve Ludtke
lecture4.pdf - Lecture 4 - Review of homework and File I/O - Steve Ludtke
pycrust-20060629-1132.py - Examples from review - Steve Ludtke
lecture6-examples.ppt - Lecture 6 notes
test2.py - Scrabble program from Lecture 6
test.py - Box file scaling example from lecture 6
pycrust-20060706-1134.py - Partial interactive session from lecture 6 - Steve Ludtke
pycrust-20060710-1112.py - Demo session from lecture 7 - Steve Ludtke
lecture7-stdlib.pdf - Lecture 7 - Standard Library - Steve Ludtke
lecture8-numbers.pdf - Lecture 8 - Numbers and CPUs - Steve Ludtke
lecture9-external.pdf - Lecture 9 - External Packages - Steve Ludtke
lecture10-eman.pdf - Lecture 10 - EMAN & Chimera - Steve Ludtke
Single Particle Reconstructions and Visualization EMAN Tutorial: Mar. 16 - Mar. 19, 2005
Presentations
Llorca.ppt - Using EMAN to obtain 3D reconstructions of asymmetric and/or small proteins - Helen Berman
final.ppt - Robbie Reutzel
EMAN_workshop_March_05_talk.ppt - Three-dimensional Reconstruction of the PA200-20S Proteasome Complex by Cryo-EM - Joaquin Ortega
Chiu_EMAN Workshop_05_03_16.pdf - Wah Chiu
Talk1.pdf - Introduction to EMAN - Steven Ludtke
Tak1.pt2.pdf - Introduction to EMAN - Pt2 - Steven Ludtke
Talk2.pdf - Model Bias and CTF Correction - Steven Ludtke
Demo1.pdf - EMAN Demo - day 1 - Steven Ludtke
Demo2.pdf - EMAN Demo - day 2 - Steven Ludtke
workshop-baker.ppt - I have a Structure, What Now? - Matthew Baker
python.pdf - EMAN - Python programming - Steven Ludtke
2005Mar17_computer_driven_microscopy.ppt - JAMES and Mr. T. - Christopher Booth
2005-SingleParticleWorkshop-Wen-Jiang.ppt - Icosahedral Reconstruction - Wen Jiang
EMANworkshop.pdf - Multiscale Structural Visualization with UCSF Chimera - Tom Ferrin
groel.pdf - Chimera Visualization Tutorial - GroEL - Thomas Goddard
semliki.pdf - Chimera Demonstration - Semliki Forest Virus - Thomas Goddard
Wrks_EMAN_Resolution_05.pdf - Resolution Criteria - Pawel Penczek
Wrks_EMAN_tomoV05.pdf - 3D Reconstruction - Pawel Penczek
Workshop of the Center of Protein Folding Machinery: Dec. 4 - Dec. 5, 2004
Presentations
Chiu_Dec workshop.ppt - Vision of the Protein Folding Machinery Project - Wah Chiu
FRYDMAN WORKSHOP 12-04.ppt - Biology and medicine of the chaperoning - Judith Frydman
J King.ppt - Genetics and Chemistry of protein folding - Jonathan King
CPF_Talk.ppt - Computational approaches in protein folding - Tanya Raschke (Michael Levitt)
Nanomedicine-Dec-2004.ppt - Crystallography of chaperoning - Paul Adams
present.ppt - Single Particle Reconstructions of GroEL, Resolution and Heterogeneity - Steven Ludtke
ChiuStanfordWorkshop4Dec04.ppt - Modeling the structures of proteins and macromolecular assemblies - Andrej Sali
Workshop-CPFMdec04.ppt - Single-Molecule Dynamical Approaches for Biological Machines - W. E. Moerner
Tanja_Kortemme.ppt - Prediction and design of protein-protein interactions - Tanja Kortemme
kwp.ppt - Simple Models of Protein Folding - Kevin Plaxco
StanfordFoldingWorkshop-2004b.ppt - Simulations of protein folding and misfolding - Vijay Pande
Presentations
07penszak.wmv - 2D Alignment and Measures of Similarity - Pawel Penczek
05penszak.wmv - 3D Reconstruction Algorithms and Resolution Measures - Pawel Penczek
06ludtke.wmv - CTF Parameterization and Correction - Steve Ludtke
08ludtke.wmv - Difficult Reconstruction Cases and EMEN - Steve Ludtke
09bakerjiang.wmv - Helixhunter and Foldhunter - Wen Jiang and Matt Baker
04chiu.wmv - Image Contrast Theory - Wah Chiu
01crowther1.wmv - Image Processing Basics I - Tony Crowther
02crowther2.wmv - Image Processing Basics II - Tony Crowther
03ludtke.wmv - Intro to EMAN - Steve Ludtke
11dougherty.wmv - Scientific Animation - Matt Dougherty
10abajaj.wmv - Scientific Visualization - Chandrajit Bajaj
Image Processing Workshop - Theory and Practice of Icosahedral Particle Reconstruction: Apr. 9, 2002
Presentations
lecture.ppt - Lecture - Tony Crowther