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| Describe WorkshopPresentationsAndVideos here. | == NCMI Workshops: Presentations and Videos Archive == |
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| Presentations and Videos go here | ''' [[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:Cryotransfer.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 |
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
Cryotransfer.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