Powerpoint presentations from Phenix developers
Here are some presentations about the Phenix software and related projects.
Pavel Afonine
- PHENIX: introduction
- Total model structure factors, bulk-solvent and overall anisotropic scaling
- Automated model partitioning into TLS groups
- Refinement (general introduction)
- phenix.refine overview (including command-line starter)
- Some Facts About Maps (version 1)
- Some Facts About Maps (version 2)
- Crystallographic Structure Validation
- Validation: cryo-EM
- Hydrogens, X-rays, neutrons and all that... (Plenary lecture, Bertaut Prize award)
- Map modification using maximum entropy method
- FEM: Feature Enhanced Map
- FAQ
- Fitting atomic models into maps: low-resolution, cryo-EM, X-ray (poster, one page)
- Real-space refinement for cryo-EM
- Communication and bug report guidelines
- Nonbonded weight
- Build water into cryo-EM maps
- Tools for cryo-EM
- Hydrogens
Tom Terwilliger
- AlphaFold changes everything (as pdf) (as pptx)
- Phenix video tutorials (various presenters)
- Cryo-EM tools in Phenix
- Brief introduction to crystallography
- Introduction to Bayesian methods in macromolecular crystallography
- MR Rosetta and morphing - ACA Trueblood lecture
- MR Rosetta
- Improving models by morphing
- Automation of structure determination
- Chain tracing
- Model building with Resolve
- Ligand building
- Building helices
- Multiple models
- Density modification
- Gordon Research Conference, July 2010
- Cold Spring Harbor, October 2010
- IIT-Bombay, February 2011
- Structure determination from weak anomalous data. GRC 30 July 2014
- Structure determination from weak anomalous data. CCP4 Study Weekend Jan 2015
- Experimental phasing, including recent developments in SAD phasing. University of Kansas Aug. 2015
- SAD phasing, model-building, density modification. Shanghai University Jan. 2016.
- SAD phasing and applications to SBGrid data. SBGrid/NECat Phenix workshop Nov. 2016.
- Cryo-EM automatic map sharpening, segmentation and model building. SBGrid/NECat Phenix workshop Nov. 2016.
- Model-building using cryo-EM maps, 2017 Model Challenge Assessment Meeting, Stanford, CA
- Model-building using cryo-EM and crystallographic maps, Understanding Biology through Structure 2017, Santa Fe, NM (video)
- Density modification and model-building with cryo-EM maps, 2020 CCP4 Study Weekend
- Density modification and model-building with cryo-EM maps, March 31, 2020 SBGrid Weekly Webinar series
Paul Adams
- Phenix Introduction, Madrid 2017
- Experimental Phasing, Madrid 2017
- Phasing Improvement, Madrid 2017
- Model Building, Madrid 2017
- Molecular Replacement, Madrid 2017
- Low Resolution Refinement, Madrid 2017
- Ensembles, Madrid 2017
- Cryo-EM Tools, Vienna 2018
- Low Resolution Refinement, Vienna 2018
- Models from Near Atomic Resolution Cryo-EM Data, Stockholm 2018
- New tools for improving electron cryo-microscopy maps and validating models, CCP-EM Symposium 2020
Oleg Sobolev
Dorothee Liebschner
- phenix.polder - A tool for calculating difference maps around atom selections by excluding the bulk solvent mask
- phenix.polder - short tutorial
- BNL workbench (October 2021) Phenix Intro
- BNL workbench (October 2021) Phenix tools for crystallography
- BNL workbench (October 2021) Alphafold MR tutorial
- 2020-01 Denver Phenix Intro
- 2020-01 Denver Phenix Map Tools
- 2020-01 Denver Model Building
- July 2022 - GRC Session intro "Divining ligands with confidence"
- West Coast Structural Biology Workshop (March 2023) "Using predicted models in Phenix"
- Rapidata (March 2023) "Planning and carrying out automated structure determination using SAD phasing"
Nat Echols
- Overview of the PHENIX GUI
- Rosetta refinement/ligand pipeline (SER-CAT workshop, Apr. 2014)
- Validation of models and maps (Argonne CCP4 workshop, June 2014)