Webinars
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Presenter: Tom Goddard, UCSF Resource for Biocomputing, Visualization, and Informatics - Topic: Using AlphaFold protein structures in ChimeraX for cryoEM modeling
Linked to presented materials: https://www.rbvi.ucsf.edu/chimerax/data/sbgrid-mar2022/alphafold_pae.html
Learn more on the ChimeraX website:
https://www.rbvi.ucsf.edu/chimerax/data/alphafold-nov2021/af_sbgrid.html
This talk was presented as part of the SBGrid Spring Mini-series - Cryo-electron microscopy of membrane proteins: from sample to structure. See the full series lineup at https://sbgrid.org/webinars/
Organized by
Prof. Jamaine Davis, Meharry Medical College
Prof. Piotr Sliz, Harvard Medical School
Prof. Patrick Sexton, ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash University
Recorded on March 29, 2022
Topic: AMPLE: a pipeline for unconventional Molecular Replacement
Presenter: Daniel Rigden, Ph.D., Reader in Post-Genome Bioinformatics, University of Liverpool, UK
Host: Jason Key
Recorded on April 26, 2016
Topic: BioGrids for SBGrid Users
Presenter: James Vincent, Ph.D., Harvard Medical School
Topic: BioGrids for SBGrid Users
BioGrids in an SBGrid-style collection of ~ 500 open source bioinformatics software titles. This software stack, which includes collections for high-throughput sequencing, genomics, proteomics, visualization, image analysis, etc, is available to all SBGrid members as an add-on option, and to all users in Harvard Medical School and Boston Children's Hospital labs as part of an institutional subscription.
Recorded on October 12, 2021
Host: Jason Key
Topic: BioXTAS RAW: An open-source program for bioSAS data analysis.
Presenter: Jesse Hopkins, Ph.D., Deputy Director, BioCAT Sector 18, Advanced Photon Source
Recorded on Jan 18, 2022
Host: Pete Meyer
Topic: Analyzing Biological Small Angle X-ray Scattering Data Using RAW
Presenter: Jesse Hopkins, Ph.D., Postdoctoral Research, Cornell University
For more information on RAW: https://sourceforge.net/projects/biox...
Host: Jason Key
Recorded on July 26, 2017
Topic: Assembling data from multiple crystals with BLEND
Presenter: James Foadi, Postdoctoral Research Associate, Diamond Synchrotron, Oxfordshire
Host: Jason Key
Recorded on February 9th, 2016
Topic: careless: Modern Machine Learning for Diffraction Data.
Presenter: Kevin Dalton, Ph.D., Hekstra Laboratory, Harvard University.
Host: Jason Key
Recorded on May 9, 2023.
For more information on careless:
- https://sbgrid.org/wiki/examples/careless.md
- https://sbgrid.org/software/titles/careless
- https://github.com/rs-station/careless-examples
Presentation Slides:
https://docs.google.com/presentation/d/1UkXy2LQJWiB-QjWkO6m-3gvA5WQShclrbdUTdTK1YTQ/edit#slide=id.p
Topic: CAVER 3.0: Analysis of Tunnels in Static and Dynamic Protein Structures
Presenter: Jan Brezovsky, Ph.D., Team Leader, Loschmidt Laboratories, Czech Republic
Host: Jason Key
Recorded on June 13, 2013
Topic: CCP4 Cloud in a nutshell and automated structure solution
Presenter: Eugene Krissinel, Ph.D., Science and Technology Facilities Council
Host: Jason Key
Recorded on February 1, 2022
Topic: CCP4 Cloud advanced: interactive MR, EP and model building
Presenter: Eugene Krissinel, Ph.D., Science and Technology Facilities Council
Hosted by Jason Key
Recorded on Feb 8, 2022
Topic: The CCP4 Molecular Graphics Program
Presenter: Stuart McNicholas, Research Fellow and CCP4-funded Developer, Dept of Chemistry, University of York
Host: Piotr Sliz
Recorded on January 24, 2013
Topic: What's new in CCP4 6.3.0
Presenter: Ronan Keegan, Ph.D., Senior Computation Scientist, CCP4 group, STFC Rutherford Appleton Laboratory
SBGrid Host: Piotr Sliz
Recorded on November 1, 2012
CCP4 website: http://www.ccp4.ac.uk
Topic: CCP-EM: software for cryo-EM
Presenter: Colin Palmer, PhD - Science and Technology Facilities Council
Recorded on May 22, 2020
Host: Shaun Rawson
Topic: Model building and validation in CCP-EM
Presenter: Colin Palmer, Computational Scientist, Science & Technology Facilities Council
Recorded on: July 23, 2019
Host: Jason Key
Topic: CcpNmr Analysis Version 3: Assign & Screen
Presenter: Vicky Higman, Ph.D., Research Fellow, University of Leicester
Host: Jason Key
Recorded on November 3, 2020
Topic: Processing serial crystallographic data using cctbx.xfel and DIALS
Presenter: Aaron Brewster, Project Scientist, Lawrence Berkeley National Laboratory
Host: Jason Key
Recorded on January 10, 2016
Topic: Making Augmented Reality Videos with ChimeraX
Presenter: Tom Goddard, University of California, San Francisco, Resource for Biocomputing, Visualization, and Informatics
The Zoom recording of this presentation is pretty choppy. We recommend you also check out the video Tom recorded and posted on his own channel here: https://youtu.be/dKNbRRRFhqY
Slides from talk available at https://www.rbvi.ucsf.edu/chimerax/data/sbgrid-july2020/
Host: Pete Meyer
Recorded on July 7, 2020
Topic: Movie Making for cryoEM using ChimeraX
Presenter: Tom Goddard, Programmer/Analyst, UCSF Resource for Biocomputing, Visualization, and Informatics
Hosted by Pete Meyer
Recorded on April 11, 2017
Topic: Cinderella
Presenter: Thorsten Wagner, Post-doctoral Fellow, Max Planck Institute of Molecular Physiology
Host: Jason Key
Recorded on March 10, 2020
Topic: What's New in Coot?
Presenter: Paul Emsley, Ph.D., MRC Laboratory of Molecular Biology
Recorded on February 16, 2021
Host: Jason Key