NCMI Workshops: Presentations and Videos Archive

Workshop on Single Particle Reconstruction, Structural Variability and Modeling: Oct 30 - Nov 2, 2015

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

Video of selected sessions Our primary video recording mechanism failed to record audio, so we unfortunately have only the EMAN and Modeling tutorials recorded

• Ludtke - Workshop Introduction

• EMAN2.12 Tutorial - Part 1 (session starts at 4:20 in video)

• EMAN2.12 Tutorial - Part 2 - 2-D Class averages

• EMAN2.12 Tutorial - Part 3 - Starting your first refinement

• EMAN2.12 Tutorial - Part 4 - Looking at the results of the first refinement

• Compositional and conformational variability in EMAN2.12 - Part 1

• Compositional and conformational variability in EMAN2.12 - Part 2

• Baker - Model building tutorial

Tutorial PDFs

• EMAN2-12_Tutorial.pdf

• EMAN2-12_Tutorial2_heterogeneity.pdf

  • Please note that e2refine_split has been improved significantly since 2.12. Suggest an update if using this method.

• Segger Tutorials

• PathwalkerGorgonTutorial.pdf

• ModelOptimizationTutorial.pdf

• ModelValidationTutorial.pdf

Tutorial Data You will also need all of the demonstration data, which we will use when going through the tutorials:

• Bgal.zip

• ribosome.zip

• segger_workshop_files.zip

• sparx_sorting.tgz

• Data-Sets.zip from Gorgon site

• sparx_ctf.tgz - NEW

• Optimize-tutorial.zip

• Validate-tutorial.zip

Completed Tutorial Projects (large files)

• Bgal-completed-tutorial.zip Result of EMAN high res tutorial (warning, 6 GB download)

• ribosome_Relion.zip Result of Relion tutorial

• Optimize_Results.zip

Software used at the workshop:

• EMAN/SPARX 2.12 (or snapshot version released after Oct. 19, 2015) - (day 1 - 2) Required. Do not use an older version.

• Relion 1.4 (optional, day 2-3) - The Relion session will largely be a demo. See comments below.

• Chimera Daily Build Oct. 17 or later - For PDB viewing and Segger tutorial (day 4, specific version required)

• Warning: we are aware of an issue with Gorgon on Ubuntu. Will remove this warning when resolved. Other Linux variants should be fine, now.

• Gorgon - Gorgon Tutorial (day 4) Please install the appropriate binary AND Data-Sets.zip

• Phenix - (end of day 4) real-space refinement of models

• LKH Solver - (day 4 - pathwalker), required only for the pathwalker tutorial, see below

• OpenMPI and PyDusa (day 2-3) SPARX tutorial may also largely be a demo, see below

Additional information and tips about software installation

These are not additional downloads, but rather are links which may assist in installing some of the required packages above.

• Please insure that you meet the specific version requirements above for each software package. Tutorials will be tested only on these specific versions.
• Mac users - If you are running El Capitan on your Mac (10.11) you will find there are a few bugs specific to this OS version we have not managed to fix yet. It should still be possible to complete the tutorial, but you will encounter a few annoyances.

• OpenMPI/Pydusa - Most SPARX tasks require MPI to run correctly, and are normally used on clusters. It is possible to install MPI on a single laptop/desktop as well, and requires minimal work or configuration to do so, you will simply be limited to the number of CPUs available on your laptop. Much of the SPARX presentation will be 'demo style' rather than a formal tutorial anyway, so you will not miss too much if you don't get MPI configured. Instructions are available here.

• Due to the required computation for most Relion refinements, Sjors plans to run a demo-style session rather than a tutorial. However, if you install Relion, you may be able to experiment with it a bit during the session. This is recommended only for users with Linux on their laptops.
• Chimera and Phenix have some restrictions on commercial use. If you work for a commercial entity, and your IT group will not install these packages, you will still be able to directly participate in most of the workshop. Phenix will only be used at the very end of day 4 to learn about real-space refinement. Chimera will be used on day 4 for a segmentation tutorial. It is also a useful utility to have available, but should otherwise not be strictly required.

• Warning - there may be some minor issues with EMAN/SPARX 2.12 on MacOS ElCapitan. If you have not upgraded, you may consider delaying until after the workshop.

• Installing EMAN2/SPARX:

  • Instructions are here: http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall

• Installing Phenix:

  • Go to http://www.phenix-online.org/download/ and click request download instructions.

  • Register (http://www.phenix-online.org/phenix_request/index.cgi) with institutional email address.

  • Then an email with a password for the download will be sent to the registered email address.
  • Use the provided link and password to download the latest official release (for example: Latest official release: 1.10.1-2155 (10-06-2015)).
  • The user should then install the command line operator version for their particular operating system.

  • Unzip the downloaded file (~918MB) and follow the install instructions in the README file (you may need to use > sudo ./install). I would suggest to install in the default directory (usr/local/..).

  • Once you have successfully installed PHENIX, to set up your environment please source the phenix_env file in the phenix installation directory (as stated in the README file).
• Installing LKH Solver
  • For linux you can download source and compile using the link above
  • For the Mac
    • You can build from source if you have Xcode - or -

    • We are providing a Mac binary lkh you can 'chmod a+x lkh' then copy to /usr/local/bin (or another folder in your $PATH)

  • For Windows, there is a binary version available: http://www.akira.ruc.dk/~keld/research/LKH/lkh.exe

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

Workshop on Single Particle Reconstruction, Map Interpretation and Visualization: Dec 10 - Dec 13, 2008

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

• - Multi-Field Biomedical Visualization - Chris Johnson

• 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

Workshop of the Center of Protein Folding Machinery: Dec. 4 - Dec. 5, 2004

Presentations

• Chiu_Dec workshop.ppt - Vision of the Protein Folding Machinery Project - Wah Chiu

• FRYDMAN WORKSHOP 12-04.ppt - Biology and medicine of the chaperoning - Judith Frydman

• J King.ppt - Genetics and Chemistry of protein folding - Jonathan King

• CPF_Talk.ppt - Computational approaches in protein folding - Tanya Raschke (Michael Levitt)

• Nanomedicine-Dec-2004.ppt - Crystallography of chaperoning - Paul Adams

• present.ppt - Single Particle Reconstructions of GroEL, Resolution and Heterogeneity - Steven Ludtke

• ChiuStanfordWorkshop4Dec04.ppt - Modeling the structures of proteins and macromolecular assemblies - Andrej Sali

• Workshop-CPFMdec04.ppt - Single-Molecule Dynamical Approaches for Biological Machines - W. E. Moerner

• Tanja_Kortemme.ppt - Prediction and design of protein-protein interactions - Tanja Kortemme

• kwp.ppt - Simple Models of Protein Folding - Kevin Plaxco

• StanfordFoldingWorkshop-2004b.ppt - Simulations of protein folding and misfolding - Vijay Pande

Tutorial of TEM for Biological Cryo-Specimens: Oct. 11, 2004

Presentations

• EMtutorial.pdf - EM Tutorial (2004) - Wah Chiu

• gridClean_Li.ppt - Grid Cleaning - Zongli Li

Tutorial on CryoEM: Oct. 18, 2003

Presentations

• EM Tutorial_03_10_18.ppt - Basics of electron microscope - Wah Chiu

• EMPresentation_Glen_1018-2003.ppt - Grid for TEM - Glen Decker

• ISvitrification2003.ppt - Theory on Cryo-EM Preparation - Irina Serysheva

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

• - Illustrating Molecular Assemblies - David Goodsell

• 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

• - Structural Proteomics of Infectious Agents - David Stuart

• 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

National Center for Macromolecular Imaging Workshop on Single Particle Reconstructions and Visualization (& EMAN Tutorial): Dec. 11 - Dec. 15, 2002

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

Image Processing Workshop - Theory and Practice of Icosahedral Particle Reconstruction: Apr. 9, 2002

Presentations

• lecture.ppt - Lecture - Tony Crowther