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| ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_84|CryoEM Training Workshop: June 8, 2007]] ''' '''Presentations''' * [[attachment:CHIU CryoEM Structure mining 070617.ppt||&do=get]] - Cryo Transfer movie - Cruciano, Angela Rees, Ian * [[attachment:Cryotransfer.mov||&do=get]] - Day 1 Lecture- Overview of Cryo EM - 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 |
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''' [[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. ---- 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 |
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.
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