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| == NCMI Workshops: Presentations and Videos == == Presentations from the Workshops == |
== NCMI Workshops: Presentations and Videos Archive == |
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| ''' NCMI Workshop on Single Particle Reconstruction, Structural Variability and Modeling ''' ''' Oct 30 - Nov 2, 2015 ''' |
''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_145|Workshop on Single Particle Reconstruction, Structural Variability and Modeling: Oct 30 - Nov 2, 2015]] ''' '''Presentations''' |
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| * [[attachment:ludtke-overview.pdf||&do=get]] - Workshop Overview - Steve Ludtke | * [[attachment:ludtke-overview.pdf]] - Workshop Overview - Steve Ludtke |
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| * [[attachment:penczek-alignment.pdf||&do=get]] - 2D Alignment Theory - Pawel Penczek * [[attachment:ludtke-minitalks.pdf||&do=get]] - CTF, Refinement, other topics - Steve Ludtke |
* [[attachment:penczek-alignment.pdf]] - 2D Alignment Theory - Pawel Penczek * [[attachment:ludtke-minitalks.pdf]] - CTF, Refinement, other topics - Steve Ludtke |
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| * [[attachment:baker-model-building.pdf||&do=get]] - Model Building - Matt Baker | * [[attachment:baker-model-building.pdf]] - Model Building - Matt Baker |
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'''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 ---- |
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