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== NCMI Workshops: Presentations and Videos Archive == ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_145|Workshop on Single Particle Reconstruction, Structural Variability and Modeling: Oct 30 - Nov 2, 2015]] ''' '''Presentations''' * [[attachment:wah-introduction.pdf]] - Introduction to the Workshop and NCMI * [[attachment:ludtke-overview.pdf]] - Workshop Overview - Steve Ludtke * [[attachment:mcmullanintro.pdf]] - Electron Microscopes & Imaging Artifacts - Greg !McMullan * [[attachment:penczek-alignment.pdf]] - 2D Alignment Theory - Pawel Penczek * [[attachment:ludtke-minitalks.pdf]] - CTF, Refinement, other topics - Steve Ludtke * [[attachment:baldwin-orientation.pdf]] - Orientation and Symmetry - Phil Baldwin * [[attachment:scheres-heterogeneity.pdf]] - Methods for Heterogeneity Analysis - Sjors Scheres * [[attachment:mcmullanDetector.pdf]] - Direct Detector Technology - Greg !McMullan * [[attachment:pintilie.pdf]] - Chimera & Segger - Greg Pintilie * [[attachment:baker-model-building.pdf]] - Model Building - Matt Baker * [[attachment:lawson-challenges.pdf]] - EMDB Challenges - Cathy Lawson '''Tutorials''' * [[attachment:EMAN2-12_Tutorial.pdf||&do=get]] * [[attachment:EMAN2-12_Tutorial2_heterogeneity.pdf||&do=get]] * Please note that e2refine_split has been improved significantly since 2.12. Suggest an update if using this method. * [[http://ncmi.bcm.edu/ncmi/software/segger/docs|Segger Tutorials]] * [[attachment:PathwalkerGorgonTutorial.pdf||&do=get]] * [[attachment:ModelOptimizationTutorial.pdf||&do=get]] * [[attachment:ModelValidationTutorial.pdf||&do=get]] ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_125|Cryo-EM Workshop at the National University of Singapore: July 9 - July 13, 2012]] ''' '''Presentations''' * [[attachment:emviz.pdf]] - Map Visualization with Chimera - Tom Goddard * [[attachment:CHIU CryoEM lecture NUS workshop 2012.pdf]] - CryoEM Basics - Wah Chiu * [[attachment:Model_bias.pdf]] - Model Bias- Mini Lecture Quantitative - Steve Ludtke * [[attachment:Particle_Eval.pdf]] - Particle Analysis (mini-lecture) - Steve Ludtke * [[attachment:EMAN2_Intro.pdf]] - EMAN2 Introduction - Steve Ludtke * [[attachment:Single_Particle_Intro.pdf]] - Introduction to Single Particle Analysis - Steve Ludtke * [[attachment:Lu Gan NUS cryo-ET lecture.pdf]] - Cryo-ET Basics - Lu Gan * [[attachment:Slides_for_workshop3_handout_red.pdf]] - Single Particle Tomography slides/handout - Michael Schmid et al * [[attachment:Flagella01-07-10-2012_red.pdf]] - Trypanosome Flagella - Schmid, M, Koyfman AY, Gheiratmand L, Fu CJ, Khant HA, Huang D, He CY, Chiu W * [[attachment:CHIU CryoEM Modeling NUS-reduced.pdf]] - CHIU Modeling Lecture - Wah Chiu ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_108|Modeling of Cryo-EM map Workshop: Jan 14 - Jan 17, 2010]] ''' '''Presentations''' * [[attachment:modeling2010_tao.pdf]] - Geometric Algorithms for De Novo Modeling - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah * [[attachment:PDB_Items_for_EM.ppt||&do=get]] - PDB Items for EM (EMDB Schema) - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah * [[attachment:HoustonWorkshopJan2010-v4.ppt||&do=get]] - EM Maps and Models in EMDB/PDB - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah * [[attachment:xray-validation-for-em.ppt||&do=get]] - Applied common sense: The why, what and how of validation - Kleywegt, Gerard J. * [[attachment:Baker-workshop2010.pdf]] - De Novo Modeling with Cryo-EM Density Maps - Baker, Matthew * [[attachment:2010-01-16 NCMI Baylor Workshop 90min Sali.pdf]] - Integrative structure determination at pseudo-atomic resolution - Andrej Sali * [[attachment:2010 Jan Mesoscale CryoEM Workshop.pdf||&do=get]] - MESOSCALE MODELING OF MACROMOLECULAR MACHINES - Michael Levitt * [[attachment:EMdepoInstructions2010.doc||&do=get]] - EM Depo Instructions - Lawson, Cathy * [[attachment:Schulten1.pdf]] - Molecular Modeling Flexible Fitting 1: Introduction to Molecular Dynamics - Schulten, Klaus * [[attachment:Schulten2.pdf]] - Molecular Modeling Flexible Fitting 2: Introduction to Method - Schulten, Klaus * [[attachment:Schulten3.pdf]] - Molecular Modeling Flexible Fitting 3: Application to Ribosome - Schulten, Klaus * [[attachment:EMD5127-3iyd.ppt||&do=get]] - Deposition example EMD-5127-PDB-3iyd - Lawson, Cathy * [[attachment:EMdepoTutorial2010.doc||&do=get]] - EM Deposition Tutorial - Lawson, Cathy * [[attachment:talk-houston_jan10-schroeder.pdf]] - Structure Refinement at Low Resolution - Schroeder, Gunnar ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_97|Structural & Computational Biomedical Informatics and Cryo-EM (UK): June 8 - June 12, 2009]] ''' '''Presentations''' * [[attachment:workflow_tutorial_final.pdf]] - EMAN2 Workflow Tutorial (Revised) - Steve Ludtke * [[attachment:Workshop_1.pdf]] - Introduction to Single Particle Reconsruction and EMAN2 - lecture notes - Steve Ludtke ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_91|Workshop on Single Particle Reconstruction, Map Interpretation and Visualization: Dec 10 - Dec 13, 2008]] ''' '''Presentations''' * [[attachment:Ludtke_1.pdf]] - Introduction to Single Particle Reconsruction and EMAN2 - Steve Ludtke * [[attachment:workflow_tutorial.pdf]] - EMAN2 Workflow Tutorial - David Woolford * [[attachment:Python_1.pdf]] - Introduction to Python - Steve Ludtke * [[attachment:berman-NCMI-dec08.ppt||&do=get]] - What the Protein Data Bank teaches us about structural biology - Berman, Helen M. * [[attachment:Wrks_EMAN2_08.pdf]] - Introduction - Penczek, Pawel * [[attachment:2008-EMAN-Wen-Jiang.pdf]] - Near-atomic resolution 3-D reconstruction of viruses - Jiang, Wen * [[attachment:2008-12-11 NCMI Baylor Workshop 60min.pdf]] - Integrating Diverse Data for Structure Determination of Macromolecular Assemblies - Andrej Sali ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_91|EMAN/Single Particle Tutorial: June 11, 2008]] ''' '''Presentations''' * [[attachment:Talk1.pdf]] - Introduction to Single Particle Reconstruction in EMAN1 - Steve Ludtke * [[attachment:Talk2-ctf.pdf]] - Introduction to Fourier Transforms and CTF Correction - Steve Ludtke * [[attachment:Demo1.pdf]] - Demo session containing walkthrough for EMAN1 DVD - Steve Ludtke * [[attachment:fits.pdf]] - FFT's Part 1 (more detailed lecture) - Steve Ludtke * [[attachment:ffts2.pdf]] - FFT's Part 2 (more detailed lecture) - Steve Ludtke ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_85|Grand challenges for Nanomedicine and Nanobiology: Aug 27, 2007]] ''' '''Presentations''' * [[attachment:ACS poster.ppt||&do=get]] - Single-walled Carbon Nanotubes in the Intact Organism:Near-IR Imaging and Biocompatibility Studies in Drosophila - Beckingham, Kathleen * [[attachment:collaboration.ppt||&do=get]] - Surfaces/nanopatterns presenting biomolecules and signaling molecules - Cai, Chengzhi * [[attachment:Suh.ppt||&do=get]] - Reengineering Adeno-Associated Virus - Suh, Junghae * [[attachment:cutaneous nanotoxicology.shs||&do=get]] - Cutaneous Nanotoxicology - Wilkerson, Michael * [[attachment:CHIU Centers 07-08-27.pdf]] - Chiu's NIH Centers at Baylor College of Medicine - Chiu, Wah * [[attachment:Introduction remark.ppt||&do=get]] - Introduction Remarks - Chiu, Wah * [[attachment:Wah Chiu action plan.ppt||&do=get]] - Action Plan - Chiu, Wah * [[attachment:Blaney.ppt||&do=get]] - Dan Duncan Cancer Center - Blaney, Susan * [[attachment:Aigner HOUSTONTALK807.ppt||&do=get]] - NIH Nanomedicine Roadmap - Aigner, Thomas * [[attachment:Judy CBEN.ppt||&do=get]] - NSF Nanotechnology - Judy Raper * [[attachment:Larry GCNN-LAN-082707 (final).ppt||&do=get]] - NCI Nanomedicine Alliance - Nagahara, Larry * [[attachment:Lee 82707.ppt||&do=get]] - NCI Nanomedicine and nano-technology - Lee, Jerry * [[attachment:Karen.ppt||&do=get]] - Recommendations: Leadership and Organization - Ethun, Karen * [[attachment:Achieving FDA approval for novel new nanomaterials.ppt||&do=get]] - Recommendations: Achieving FDA approval for novel nanomaterials - Sevick, Eva M. * [[attachment:Baylor.ppt||&do=get]] - Nanotechnology Center for Mechanics - Michael Sheetz * [[attachment:Clinical problems for nanotechnology.ppt||&do=get]] - Defining the right clinical problems for nanotechnology - Oghalai, John * [[attachment:Nano discussion.ppt||&do=get]] - Challenges for Clinical Applications of Nanotechnology - Eissa, N. Tony * [[attachment:Cell biology.ppt||&do=get]] - Recomendations: Cell Biology and Nanoscience - Sifers, Richard N. * [[attachment:nanomed-computation.ppt||&do=get]] - Recomendations: Computation and Informatics - Baker, Matthew ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_84|CryoEM Structure Mining: June 17, 2007]] ''' '''Presentations''' * [[attachment:CHIU CryoEM Structure mining 070617.ppt||&do=get]] - Introduction to cryoEM - Wah Chiu ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_83|CryoEM Training Workshop: June 8, 2007]] ''' '''Presentations''' * [[attachment:Cryo_Transfer.mov||&do=get]] - Cryo Transfer movie - Cruciano, Angela; Rees, Ian * [[attachment:Chiu handout 1 07-06-08.ppt||&do=get]] - Day 1 Lecture- Overview of Cryo EM - Wah Chiu * [[attachment:MDS Alignment.ppt||&do=get]] - MDS alignment - Cruciano, Angela ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_66|Workshop on Single Particle Reconstruction and Visualization: Mar. 14, 2007]] ''' '''Presentations''' * [[attachment:houston_march07.ppt||&do=get]] - EMdep: Deposition EM maps - Kim Henrick * [[attachment:Chiu_EMAN Contrast theory_07_03-15.pdf]] - Image Contrast Theory - Wah Chiu * [[attachment:2007-EMAN-Workshop-Wen-Jiang.pdf]] - Icosahedral Reconstruction - Jiang, Wen * [[attachment:EMANworkshop-Ferrin.pdf||&do=get]] - Visualization tools for complex biological structures - Tom Ferrin * [[attachment:chimera-eman-2007.pdf]] - Chimera Tutorial - Tom Goddard * [[attachment:ianrees_emen2_mar8.pdf]] - EMEN2: An Extensible, Collaborative, Electronic Lab Notebook - Rees, Ian * [[attachment:EMAN-workshop07-AIRS.ppt||&do=get]] - VIsualizing and Analyzing CryoEM Density Maps with AIRS - Matthew Baker * [[attachment:EMAN_Wkshp_MFS_Handout.ppt||&do=get]] - Aligning and Averaging 3-D Subvolumes from Electron Cryo-Tomograms - Schmid, Michael * [[attachment:Fourier Transforms.ppt||&do=get]] - Fourier Transforms, Filtering and Convolution - Marsh, Mike * [[attachment:updated_Wrks_EMAN_07.pdf||&do=get]] - updated Image similariry measures and such - Pawel A. Penczek * [[attachment:PmvVision.pdf]] - A Brief Introduction to PMV-VIsion - Zhao, Yong; Sanner, Michel * [[attachment:EMAN_CM_Modeller.ppt||&do=get]] - Introduction to comparative modeling with MODELLER (final version) - Webb, Ben and Topf, Maya * [[attachment:EMAN_Modeller_hands_on.ppt||&do=get]] - MODELLER hands-on session (final version) - Webb, Ben and Topf, Maya * [[attachment:EMANDemo1.pdf]] - EMAN Practical Session Slides - Ludtke, Steven * [[attachment:python_intro.pdf]] - Introduction to Python - Ludtke, Steven * [[attachment:talk1-intro.pdf]] - Workshop Welcome and Single Particle Reconstruction Overview - Ludtke, Steven * [[attachment:talk2-ctf.pdf]] - CTF Correction, Resolution Measurement & Model Bias - Ludtke, Steven ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_64|CryoEM Workshop: Oct. 17, 2006]] ''' '''Presentations''' * [[attachment:2006Oct18CryoEMCourseCCDs.ppt||&do=get]] - Introduction To Using CCD Cameras In cryo-EM - Booth, Christopher * [[attachment:CHIU Handout CryoEM Rice 06-10-18.ppt||&do=get]] - CryoEM Lecture for Biophysics Course and Workshop on Oct 18 2006 - Wah Chiu * [[attachment:Cryo TEM from specimen prep to the microscope_Gatan Presentation_LAM1.pdf]] - Cryo TEM from specimen prep to the microscope - Linda Melanson * [[attachment:CryoEM_Imaging_NCMI_20061018.pdf||&do=get]] - Imaging in Cryo-electron microscopy - Brink, Jaap * [[attachment:Frederik.pdf]] - CryoEM of supsension - Professor Peter Frederik ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_60|Introduction to Programming for Scientists Lecture Series: Jun. 12, 2006]] ''' '''Presentations''' * [[attachment:lecture1.pdf]] - Lecture 1 - Simple Datatypes - Steve Ludtke * [[attachment:lecture2.pdf]] - Lecture 2 - Lists, Tuples and Dictionaries - Steve Ludtke * [[attachment:lecture3.pdf ]] - Lecture 3 - if, while, for - Steve Ludtke * [[attachment:lecture4.pdf]] - Lecture 4 - Review of homework and File I/O - Steve Ludtke * [[attachment:pycrust-20060629-1132.py||&do=get]] - Examples from review - Steve Ludtke * [[attachment:lecture6-examples.ppt||&do=get]] - Lecture 6 notes * [[attachment:test2.py||&do=get]] - Scrabble program from Lecture 6 * [[attachment:test.py||&do=get]] - Box file scaling example from lecture 6 * [[attachment:pycrust-20060706-1134.py||&do=get]] - Partial interactive session from lecture 6 - Steve Ludtke * [[attachment:pycrust-20060710-1112.py||&do=get]] - Demo session from lecture 7 - Steve Ludtke * [[attachment:lecture7-stdlib.pdf]] - Lecture 7 - Standard Library - Steve Ludtke * [[attachment:lecture8-numbers.pdf]] - Lecture 8 - Numbers and CPUs - Steve Ludtke * [[attachment:lecture9-external.pdf]] - Lecture 9 - External Packages - Steve Ludtke * [[attachment:lecture10-eman.pdf]] - Lecture 10 - EMAN & Chimera - Steve Ludtke ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_52|Visualization of Large Biomolecular Complexes: Sep. 11 - Sep. 13, 2005]] ''' '''Presentations''' * [[attachment:]] - Multi-Field Biomedical Visualization - Chris Johnson * [[attachment:EllipsoidMolecules.ppt||&do=get]] - Hierarchical Molecular Modelling with Ellipsoids - Nelson Max * [[attachment:Moreland_AltReps.ppt||&do=get]] - Alternative Representations for Biological Complexes - John L. Moreland * [[attachment:Lawson_2005_vis_workshop.ppt||&do=get]] - Visualisation of Large Biomolecular Complexes - Lawson, Cathy * [[attachment:SanDiego.ppt||&do=get]] - Hierarchical Molecular Modelling with Ellipsoids: long version - Nelson Max * [[attachment:PPInterfaces_FCazals_VLBC.pdf||&do=get]] - Revisiting the description of Protein-Protein interfaces - F. Cazals * [[attachment:]] - Software Components for Modeling Large Bimolecular Complexes - Michel Sanner * [[attachment:chimera-sep2005.pdf||&do=get]] - Exploring Large Molecular Complexes with UCSF Chimera - Tom Goddard * [[attachment:MBaker-visworkshop.ppt||&do=get]] - Visualization and Analysis of Macromolecular Complexes - Baker, Matthew * [[attachment:Varshney05.ppt||&do=get]] - Molecular Visualization: Advances and Challenges - Varshney, Amitabh * [[attachment:snoeyink-biomolecvis05.ppt||&do=get]] - Geometric algorithms in biomolecular visualization & analysis - Jack Snoeyink * [[attachment:delano_pymol.ppt||&do=get]] - Is PyMOL Ready to Handle Large Biomolecular Complexes? - DeLano, Warren L. * [[attachment:2005_09_12_Bajaj_Alg_Talk.pdf]] - Geometric and Signal 3D Processing and some Visualization - Bajaj, Chandra * [[attachment:2005_taylor_bimolecular_v2.ppt||&do=get]] - Displaying Two Intimate Surfaces, multiple scalar fields, etc - Russell M. Taylor II, Chris Weigle, Alexandra Bokinsky, David Borland, others. * [[attachment:vmdvlbc2005.ppt||&do=get]] - VMD: Algorithms and Methods for Visualizing Large Biomolecular Complexes - Stone, John * [[attachment:bio-visualization.ppt||&do=get]] - Visualization Wish lists - Vijay Reddy * [[attachment:NIH-Biovisualization05-Johnson.ppt||&do=get]] - Biomedical Visualization and Software Frameworks - Chris Johnson * [[attachment:Breakout_Implementation.doc||&do=get]] - Break out Group Implementation - All * [[attachment:BreakOut_Algorithms.doc||&do=get]] - Break out Group Algorithms - All * [[attachment:ActionItems.doc||&do=get]] - Action Items - All * [[attachment:Agenda_for_Vis-workshop.doc||&do=get]] - Final Final Agenda - All * [[attachment:2005VisPresentation.ppt||&do=get]] - Molecular Illustration from Atoms to Cells - Goodsell, David S. * [[attachment:VisWorkshop.ppt||&do=get]] - Software Components for Modeling Large Biomolecular Complexes - Sanner, Michel * [[attachment:Baker, T. Powerpoint.ppt||&do=get]] - Challenges in the Visualization, Analysis, and Interpretation of Large Macromolecular Complexes - Tim S. Baker ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_53|CryoEM Tutorial: Jul. 25 - Jul. 29, 2005]] ''' '''Presentations''' * [[attachment:cryoEM workshop 05_07_26.ppt||&do=get]] - Basics of CryoEM - Wah Chiu * [[attachment:cryo_EM-workshop_7-25-05.ppt||&do=get]] - EM grid preparation - Zongli Li * [[attachment:cryoEM2005_Serysheva.ppt||&do=get]] - Vitrification of biological specimen - Serysheva, Irina * [[attachment:2005July26_DetectingElectronsLecture.ppt||&do=get]] - Detecting Electrons: CCD vs Film - Christopher Booth ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_49|Workshop on Structural and Computational Proteomics of Biological Complexes: May. 16 - May. 17, 2005]] ''' '''Presentations''' * [[attachment:Baylor.ppt||&do=get]] - Data Management in the Protein Data Bank - Oscar Llorca * [[attachment:Structural Biology Workshop-Jacobson.mov||&do=get]] - Purification of S. Cerevisiae TFIID for Structural Studies - Raymond Jacobson * [[attachment:wenselwkshp05my.ppt||&do=get]] - Structural Dynamics of Signal-Transducing Membrane Complexes - Theodore Wensel * [[attachment:CHIU_Workshop Intro_05_05_16.ppt||&do=get]] - Worskhop Introduction - Wah Chiu * [[attachment:emen2.ppt||&do=get]] - EMEN2 - A Distributed Object-oriented Electronic Notebook for Data Archival, Sharing and Mining - Steven Ludtke * [[attachment:CCBC2005.ppt||&do=get]] - Modeling Platform for Collaboration - Zheng Li * [[attachment:tdavisHoustonupload2005.ppt||&do=get]] - The Lattice Structure of the Yeast Spindle Pole Body Probed by Fluorescence Resonance Energy Transfer - Trisha Davis * [[attachment:markley_sesame_dep.ppt||&do=get]] - Sesame: a Data Management System for Structural Proteomics - John Markley * [[attachment:DASH-C2BCworkshop.pdf||&do=get]] - Enhancing Data Sharing in Collaborative Research Projects with DASH - Thomas Ferrin * [[attachment:ChiuWorkshop Houston17May05.pdf||&do=get]] - EMEN2 - Modeling the structures of proteins and macromolecular assemblies - Andrej Sali * [[attachment:baylor.pdf||&do=get]] - Computational study of the binding specificities of SH2 and SH3 domains - Wei Wang * [[attachment:Baylor talk.ppt||&do=get]] - Structural Investigations of Herpesvirus Infection. - Frazer Rixon * [[attachment:Houston2005-1.ppt||&do=get]] - Center for Genomic Experimentation and Computation - Orna Resnekov ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_7|Single Particle Reconstructions and Visualization EMAN Tutorial: Mar. 16 - Mar. 19, 2005]] ''' '''Presentations''' * [[attachment:Llorca.ppt||&do=get]] - Using EMAN to obtain 3D reconstructions of asymmetric and/or small proteins - Helen Berman * [[attachment:final.ppt ||&do=get]] - Robbie Reutzel * [[attachment:EMAN_workshop_March_05_talk.ppt||&do=get]] - Three-dimensional Reconstruction of the PA200-20S Proteasome Complex by Cryo-EM - Joaquin Ortega * [[attachment:Chiu_EMAN Workshop_05_03_16.pdf||&do=get]] - Wah Chiu * [[attachment:Talk1.pdf||&do=get]] - Introduction to EMAN - Steven Ludtke * [[attachment:Tak1.pt2.pdf||&do=get]] - Introduction to EMAN - Pt2 - Steven Ludtke * [[attachment:Talk2.pdf||&do=get]] - Model Bias and CTF Correction - Steven Ludtke * [[attachment:Demo1.pdf||&do=get]] - EMAN Demo - day 1 - Steven Ludtke * [[attachment:Demo2.pdf||&do=get]] - EMAN Demo - day 2 - Steven Ludtke * [[attachment:workshop-baker.ppt||&do=get]] - I have a Structure, What Now? - Matthew Baker * [[attachment:python.pdf||&do=get]] - EMAN - Python programming - Steven Ludtke * [[attachment:2005Mar17_computer_driven_microscopy.ppt||&do=get]] - JAMES and Mr. T. - Christopher Booth * [[attachment:2005-SingleParticleWorkshop-Wen-Jiang.ppt||&do=get]] - Icosahedral Reconstruction - Wen Jiang * [[attachment:EMANworkshop.pdf||&do=get]] - Multiscale Structural Visualization with UCSF Chimera - Tom Ferrin * [[attachment:groel.pdf||&do=get]] - Chimera Visualization Tutorial - GroEL - Thomas Goddard * [[attachment:semliki.pdf||&do=get]] - Chimera Demonstration - Semliki Forest Virus - Thomas Goddard * [[attachment:Wrks_EMAN_Resolution_05.pdf||&do=get]] - Resolution Criteria - Pawel Penczek * [[attachment:Wrks_EMAN_tomoV05.pdf||&do=get]] - 3D Reconstruction - Pawel Penczek ---- |
NCMI Workshops: Presentations and Videos Archive
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_Tutorial2_heterogeneity.pdf
- Please note that e2refine_split has been improved significantly since 2.12. Suggest an update if using this method.
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
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
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
CryoEM Tutorial: Jul. 25 - Jul. 29, 2005
Presentations
cryoEM workshop 05_07_26.ppt - Basics of CryoEM - Wah Chiu
cryo_EM-workshop_7-25-05.ppt - EM grid preparation - Zongli Li
cryoEM2005_Serysheva.ppt - Vitrification of biological specimen - Serysheva, Irina
2005July26_DetectingElectronsLecture.ppt - Detecting Electrons: CCD vs Film - Christopher Booth
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