AlphaFold protein structures & ChimeraX cryoEM modeling

  • 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:

    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

    BioGrids for SBGrid Users

  • 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:

    CAVER 3.0

  • 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

    CCP4 Cloud Part I

  • 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

    CCP4 Cloud Part II

  • 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

    CCP4 Molecular Graphics (CCP4-MG)

  • 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

    CCP4 Version 6.3.0

  • 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