NCMI Workshops: Cryo EM Modeling
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
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
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
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
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
Visualization of Biological Complexes: Oct. 11 - Oct. 12, 2003
Presentations
Chiu_Visualization_workshop.ppt - Workshop Goals - Wah Chiu
Sali Assemblies Wah 11Oct03.ppt - Modeling of macromolecular assemblies - Andrej Sali
Jiang_Baker_sf2003.ppt - Structural Feature Extraction in Intermediate Resolution Macromolecular Assemblies - Matthew Baker
Goddard-PDB-Viruses-2003.pdf - Data Quality Problems in PDB Virus Models - Tom Goddard (Michael Levitt)
Bajaj_2003_10_11_BerkeleyWorkshop.pdf - Quantitative Visualization of Static and Dynamic Biological Complexes - Chandrajit Bajaj
FerrinMultiscale03.pdf - Multiscale Structural Visualization with UCSF Chimera - Thomas Ferrin
Carazo-NIH-Oct-2003.ppt - Unreveiling new biological knowledge from multiresolution structural proteomics data - Jose-Maria Carazo
Berman_visualization2.ppt - Protein Data Bank Challenges - Shuchismita Dutta
Jiang_Baker_sf2003.ppt - Structural Feature Extraction in Intermediate Resolution Macromolecular Assemblies - Wen Jiang
delano_pymol.ppt - Issues Surrounding the Use of Open-Source PyMOL to Visualize Large Complexes - Warren Delano
OlsonBerkeley-03-talk.ppt - Advanced User Interfaces - Back to the Future ? - Arthur J. Olson
Sanner.ppt - Representation, Implementation, and Interaction: Challenges for Macromolecular Assemblies - Michel Sanner
BioCompVis_2003.ppt - MBT - The Molecular Biology Toolkit - John Moreland
Dougherty_Visualization workshop.ppt - Visualization activities at NCMI - Matthew Dougherty
- Building visualization and analysis applications using Molecular Biology Toolkit - Sasha Buzko
Apostol_Draft.ppt - The Molecular Biology Toolkit - Geometry Engine Capabilities - Apostle Gramada
Workshop on Structural Proteomics of Biological Complexes: Apr. 7 - Apr. 8, 2003
Presentations
Chiu_Visualization_workshop.ppt - Workshop Goals - Wah Chiu
Drubin.ppt - Why Studying Large Protein Complexes is Crucial at this Time - David Drubin
Jack Greenblatt.ppt - Protein Complexes in Transcription - Jack Greenblatt
- Chromosome Segregation and Kinetochore Structure in Yeast - Peter K. Sorger
- Protein Complexes in Cell Division in Eggs from Xenopus Laevis - Rebecca Heald
Yates.ppt - Analysis of Protein Complexes by Mass Spectrometry - John Yates
Boone.ppt - Synthetic Genetic Array Analysis: Large-Scale Mapping of Genetic Interactions Networks in Yeast - Charlie Boone
- Mining Relevance from the Mycobacterium Tuberculosis Genome and Structural Database - William Jacobs
Gerstein.ppt - Computational Proteomics: Prediction of Protein Interactions and Function on a Genome-Scale - Mark Gerstein
Sali.ppt - Modeling the Structures of Molecular Assemblies by Satisfaction of Spatial Restraints - Andrej Sali
Downing.ppt - Electron Crystallography: Current State and Prospects - Ken Downing
Milligan.ppt - The Combined Use of Cryo-Electron Microscopy and X-Ray Crystallography to Understand the Structure and Mechanisms of Molecular Machines - Ron Milligan
Almo.ppt - Structural Proteomics: Structural Dissection of Protein Machines - Steve Almo
Kurosky.ppt - Proteomics in Airway Inflammation - Alex Kurosky
Buchanan.ppt - New Approaches for High-Throughput Identification and Characterization of Protein Complexes - Michelle Buchanan
Davis.ppt - Yeast Resource Center - Trisha Davis
Makowski.ppt - Realistic Goals and Milestones; Resources Needed and Funding Mechanisms - Lee Makowski
Presentations
07penszak.wmv - 2D Alignment and Measures of Similarity - Pawel Penczek
05penszak.wmv - 3D Reconstruction Algorithms and Resolution Measures - Pawel Penczek
06ludtke.wmv - CTF Parameterization and Correction - Steve Ludtke
08ludtke.wmv - Difficult Reconstruction Cases and EMEN - Steve Ludtke
09bakerjiang.wmv - Helixhunter and Foldhunter - Wen Jiang and Matt Baker
04chiu.wmv - Image Contrast Theory - Wah Chiu
01crowther1.wmv - Image Processing Basics I - Tony Crowther
02crowther2.wmv - Image Processing Basics II - Tony Crowther
03ludtke.wmv - Intro to EMAN - Steve Ludtke
11dougherty.wmv - Scientific Animation - Matt Dougherty
10abajaj.wmv - Scientific Visualization - Chandrajit Bajaj