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.

Stone, John VMD: Algorithms and Methods for Visualizing Large Biomolecular Complexes vmdvlbc2005.ppt Vijay Reddy Visualization Wish lists bio-visualization.ppt Chris Johnson Biomedical Visualization and Software Frameworks NIH-Biovisualization05-Johnson.ppt All Break out Group Implementation Breakout_Implementation.doc All Break out Group Algorithms BreakOut_Algorithms.doc All Action Items ActionItems.doc All Final Final Agenda Agenda_for_Vis-workshop.doc Goodsell, David S. Molecular Illustration from Atoms to Cells 2005VisPresentation.ppt Sanner, Michel Software Components for Modeling Large Biomolecular Complexes VisWorkshop.ppt Tim S. Baker Challenges in the Visualization, Analysis, and Interpretation of Large Macromolecular Complexes Baker, T. Powerpoint.ppt