NCMI Workshops: Cryo EM Modeling
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
Modeling of Cryo-EM map Workshop: Jan 14 - Jan 17, 2010
Presentations
modeling2010_tao.pdf - Geometric Algorithms for De Novo Modeling - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah
PDB_Items_for_EM.ppt - PDB Items for EM (EMDB Schema) - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah
HoustonWorkshopJan2010-v4.ppt - EM Maps and Models in EMDB/PDB - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah
xray-validation-for-em.ppt - Applied common sense: The why, what and how of validation - Kleywegt, Gerard J.
Baker-workshop2010.pdf - De Novo Modeling with Cryo-EM Density Maps - Baker, Matthew
2010-01-16 NCMI Baylor Workshop 90min Sali.pdf - Integrative structure determination at pseudo-atomic resolution - Andrej Sali
2010 Jan Mesoscale CryoEM Workshop.pdf - MESOSCALE MODELING OF MACROMOLECULAR MACHINES - Michael Levitt
EMdepoInstructions2010.doc - EM Depo Instructions - Lawson, Cathy
Schulten1.pdf - Molecular Modeling Flexible Fitting 1: Introduction to Molecular Dynamics - Schulten, Klaus
Schulten2.pdf - Molecular Modeling Flexible Fitting 2: Introduction to Method - Schulten, Klaus
Schulten3.pdf - Molecular Modeling Flexible Fitting 3: Application to Ribosome - Schulten, Klaus
EMD5127-3iyd.ppt - Deposition example EMD-5127-PDB-3iyd - Lawson, Cathy
EMdepoTutorial2010.doc - EM Deposition Tutorial - Lawson, Cathy
talk-houston_jan10-schroeder.pdf - Structure Refinement at Low Resolution - Schroeder, Gunnar
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
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
Visualization of Large Biomolecular Complexes: Sep. 11 - Sep. 13, 2005
Presentations
EllipsoidMolecules.ppt - Hierarchical Molecular Modelling with Ellipsoids - Nelson Max
Moreland_AltReps.ppt - Alternative Representations for Biological Complexes - John L. Moreland
Lawson_2005_vis_workshop.ppt - Visualisation of Large Biomolecular Complexes - Lawson, Cathy
SanDiego.ppt - Hierarchical Molecular Modelling with Ellipsoids: long version - Nelson Max
PPInterfaces_FCazals_VLBC.pdf - Revisiting the description of Protein-Protein interfaces - F. Cazals
- Software Components for Modeling Large Bimolecular Complexes - Michel Sanner
chimera-sep2005.pdf - Exploring Large Molecular Complexes with UCSF Chimera - Tom Goddard
MBaker-visworkshop.ppt - Visualization and Analysis of Macromolecular Complexes - Baker, Matthew
Varshney05.ppt - Molecular Visualization: Advances and Challenges - Varshney, Amitabh
snoeyink-biomolecvis05.ppt - Geometric algorithms in biomolecular visualization & analysis - Jack Snoeyink
delano_pymol.ppt - Is PyMOL Ready to Handle Large Biomolecular Complexes? - DeLano, Warren L.
2005_09_12_Bajaj_Alg_Talk.pdf - Geometric and Signal 3D Processing and some Visualization - Bajaj, Chandra
2005_taylor_bimolecular_v2.ppt - Displaying Two Intimate Surfaces, multiple scalar fields, etc - Russell M. Taylor II, Chris Weigle, Alexandra Bokinsky, David Borland, others.
vmdvlbc2005.ppt - VMD: Algorithms and Methods for Visualizing Large Biomolecular Complexes - Stone, John
bio-visualization.ppt - Visualization Wish lists - Vijay Reddy
NIH-Biovisualization05-Johnson.ppt - Biomedical Visualization and Software Frameworks - Chris Johnson
Breakout_Implementation.doc - Break out Group Implementation - All
BreakOut_Algorithms.doc - Break out Group Algorithms - All
ActionItems.doc - Action Items - All
Agenda_for_Vis-workshop.doc - Final Final Agenda - All
2005VisPresentation.ppt - Molecular Illustration from Atoms to Cells - Goodsell, David S.
VisWorkshop.ppt - Software Components for Modeling Large Biomolecular Complexes - Sanner, Michel
Baker, T. Powerpoint.ppt - Challenges in the Visualization, Analysis, and Interpretation of Large Macromolecular Complexes - Tim S. Baker
Workshop on Structural and Computational Proteomics of Biological Complexes: May. 16 - May. 17, 2005
Presentations
Baylor.ppt - Data Management in the Protein Data Bank - Oscar Llorca
Structural Biology Workshop-Jacobson.mov - Purification of S. Cerevisiae TFIID for Structural Studies - Raymond Jacobson
wenselwkshp05my.ppt - Structural Dynamics of Signal-Transducing Membrane Complexes - Theodore Wensel
CHIU_Workshop Intro_05_05_16.ppt - Worskhop Introduction - Wah Chiu
emen2.ppt - EMEN2 - A Distributed Object-oriented Electronic Notebook for Data Archival, Sharing and Mining - Steven Ludtke
CCBC2005.ppt - Modeling Platform for Collaboration - Zheng Li
tdavisHoustonupload2005.ppt - The Lattice Structure of the Yeast Spindle Pole Body Probed by Fluorescence Resonance Energy Transfer - Trisha Davis
markley_sesame_dep.ppt - Sesame: a Data Management System for Structural Proteomics - John Markley
DASH-C2BCworkshop.pdf - Enhancing Data Sharing in Collaborative Research Projects with DASH - Thomas Ferrin
ChiuWorkshop Houston17May05.pdf - EMEN2 - Modeling the structures of proteins and macromolecular assemblies - Andrej Sali
baylor.pdf - Computational study of the binding specificities of SH2 and SH3 domains - Wei Wang
Baylor talk.ppt - Structural Investigations of Herpesvirus Infection. - Frazer Rixon
Houston2005-1.ppt - Center for Genomic Experimentation and Computation - Orna Resnekov
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
Visualization of Biological Complexes: Oct. 11 - Oct. 12, 2003
Presentations
Chiu_Visualization_workshop.ppt - Workshop Goals - Wah Chiu
Sali Assemblies Wah 11Oct03.ppt - Modeling of macromolecular assemblies - Andrej Sali
Jiang_Baker_sf2003.ppt - Structural Feature Extraction in Intermediate Resolution Macromolecular Assemblies - Matthew Baker
Goddard-PDB-Viruses-2003.pdf - Data Quality Problems in PDB Virus Models - Tom Goddard (Michael Levitt)
Bajaj_2003_10_11_BerkeleyWorkshop.pdf - Quantitative Visualization of Static and Dynamic Biological Complexes - Chandrajit Bajaj
FerrinMultiscale03.pdf - Multiscale Structural Visualization with UCSF Chimera - Thomas Ferrin
Carazo-NIH-Oct-2003.ppt - Unreveiling new biological knowledge from multiresolution structural proteomics data - Jose-Maria Carazo
Berman_visualization2.ppt - Protein Data Bank Challenges - Shuchismita Dutta
Jiang_Baker_sf2003.ppt - Structural Feature Extraction in Intermediate Resolution Macromolecular Assemblies - Wen Jiang
delano_pymol.ppt - Issues Surrounding the Use of Open-Source PyMOL to Visualize Large Complexes - Warren Delano
OlsonBerkeley-03-talk.ppt - Advanced User Interfaces - Back to the Future ? - Arthur J. Olson
Sanner.ppt - Representation, Implementation, and Interaction: Challenges for Macromolecular Assemblies - Michel Sanner
BioCompVis_2003.ppt - MBT - The Molecular Biology Toolkit - John Moreland
Dougherty_Visualization workshop.ppt - Visualization activities at NCMI - Matthew Dougherty
- Building visualization and analysis applications using Molecular Biology Toolkit - Sasha Buzko
Apostol_Draft.ppt - The Molecular Biology Toolkit - Geometry Engine Capabilities - Apostle Gramada
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
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
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