NCMI Workshops: Cryo EM Image Processing
Click above for the Workshop presentations
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