NCMI Workshops: Presentations and Videos Archive

Workshop on Single Particle Reconstruction, Structural Variability and Modeling: Oct 30 - Nov 2, 2015

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

Tutorials

• 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

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

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

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

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

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

CryoEM Workshop: Oct. 17, 2006

Presentations

• 2006Oct18CryoEMCourseCCDs.ppt - Introduction To Using CCD Cameras In cryo-EM - Booth, Christopher

• CHIU Handout CryoEM Rice 06-10-18.ppt - CryoEM Lecture for Biophysics Course and Workshop on Oct 18 2006 - Wah Chiu

• Cryo TEM from specimen prep to the microscope_Gatan Presentation_LAM1.pdf - Cryo TEM from specimen prep to the microscope - Linda Melanson

• CryoEM_Imaging_NCMI_20061018.pdf - Imaging in Cryo-electron microscopy - Brink, Jaap

• Frederik.pdf - CryoEM of supsension - Professor Peter Frederik

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

Visualization of Large Biomolecular Complexes: Sep. 11 - Sep. 13, 2005

Presentations

• - Multi-Field Biomedical Visualization - Chris Johnson

• 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