Phenix Tutorials

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Welcome to Phenix! See Playlists for all of our videos by category. PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Comments are pre-moderated. So if you want to leave feed-back but do not want it to be published and visible to everyone, mention this in your comment.

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Using AlphaFold predictions for structure determination (Tom Terwilliger)

Using AlphaFold predictions for structure determination (Tom Terwilliger) Phenix Tutorials

845 views - 1 year ago

Molecular Replacement and cryo-EM docking (Randy Read)

Molecular Replacement and cryo-EM docking (Randy Read) Phenix Tutorials

533 views - 1 year ago

Refinement X-ray and cryo-EM (Pavel Afonine)

Refinement X-ray and cryo-EM (Pavel Afonine) Phenix Tutorials

1.2K views - 1 year ago

Ligand restraints (Nigel Moriarty)

Ligand restraints (Nigel Moriarty) Phenix Tutorials

347 views - 1 year ago

Model Validation (Christopher Williams)

Model Validation (Christopher Williams) Phenix Tutorials

356 views - 1 year ago

T. Terwilliger: Alpha Fold Changes Everything (IUCR 2023 keynote lecture)

T. Terwilliger: Alpha Fold Changes Everything (IUCR 2023 keynote lecture) Phenix Tutorials

2.3K views - 2 years ago

Cryo-EM structure determination with AlphaFold using PredictAndBuild

Cryo-EM structure determination with AlphaFold using PredictAndBuild Phenix Tutorials

1.9K views - 2 years ago

X-ray structure determination with AlphaFold using PredictAndBuild

X-ray structure determination with AlphaFold using PredictAndBuild Phenix Tutorials

1.3K views - 2 years ago

How to run AlphaFold prediction in Phenix

How to run AlphaFold prediction in Phenix Phenix Tutorials

1.5K views - 2 years ago

Structure determination with AlphaFold in Phenix

Structure determination with AlphaFold in Phenix Phenix Tutorials

1.4K views - 2 years ago

Running Emplace_local via ChimeraX

Running Emplace_local via ChimeraX Phenix Tutorials

4.1K views - 2 years ago

Running Phenix via ChimeraX: setup

Running Phenix via ChimeraX: setup Phenix Tutorials

2.1K views - 2 years ago

Using Xtricorder and Xtriage from HKLviewer for inspecting TNCS, anisotropy and twinning.

Using Xtricorder and Xtriage from HKLviewer for inspecting TNCS, anisotropy and twinning. Phenix Tutorials

401 views - 3 years ago

HKLViewer demonstration

HKLViewer demonstration Phenix Tutorials

381 views - 4 years ago

Tom Terwilliger: AlphaFold changes everything

Tom Terwilliger: AlphaFold changes everything Phenix Tutorials

3.2K views - 4 years ago

HKLViewer demonstration

HKLViewer demonstration Phenix Tutorials

604 views - 4 years ago

Using an AlphaFold model for molecular replacement

Using an AlphaFold model for molecular replacement Phenix Tutorials

4.5K views - 4 years ago

Phenix Workshop 4/14/2021 (cryo-EM) - Restraints in Phenix

Phenix Workshop 4/14/2021 (cryo-EM) - Restraints in Phenix Phenix Tutorials

1.7K views - 4 years ago

Phenix Workshop 4/14/2021 (cryo-EM) - Model validation

Phenix Workshop 4/14/2021 (cryo-EM) - Model validation Phenix Tutorials

1.9K views - 4 years ago

Phenix Workshop 4/14/2021 (cryo-EM) - Real Space Refinement

Phenix Workshop 4/14/2021 (cryo-EM) - Real Space Refinement Phenix Tutorials

7.9K views - 4 years ago

Phenix Workshop 4/7/2021 (cryo-EM) - Cryo-EM map improvement

Phenix Workshop 4/7/2021 (cryo-EM) - Cryo-EM map improvement Phenix Tutorials

5.9K views - 4 years ago

Phenix Workshop 4/7/2021 (cryo-EM) - Automated model building

Phenix Workshop 4/7/2021 (cryo-EM) - Automated model building Phenix Tutorials

4.3K views - 4 years ago

Phenix Workshop 4/7/2021 (cryo-EM) - Introduction to Phenix

Phenix Workshop 4/7/2021 (cryo-EM) - Introduction to Phenix Phenix Tutorials

2.6K views - 4 years ago

Phenix Workshop 11/17/2020 (Xtallography) - Introduction to Phenix

Phenix Workshop 11/17/2020 (Xtallography) - Introduction to Phenix Phenix Tutorials

2.4K views - 5 years ago

Phenix Workshop 11/18/2020 (Xtallography) - Refinement

Phenix Workshop 11/18/2020 (Xtallography) - Refinement Phenix Tutorials

5.2K views - 5 years ago

Phenix Workshop 11/18/2020 (Xtallography) - Ligands and restraints

Phenix Workshop 11/18/2020 (Xtallography) - Ligands and restraints Phenix Tutorials

998 views - 5 years ago

Phenix Workshop 11/18/2020 (Xtallography) - Model validation

Phenix Workshop 11/18/2020 (Xtallography) - Model validation Phenix Tutorials

682 views - 5 years ago

Phenix Workshop 11/18/2020 (Xtallography) - Q&A

Phenix Workshop 11/18/2020 (Xtallography) - Q&A Phenix Tutorials

367 views - 5 years ago

Phenix Workshop 11/17/2020 (Xtallography) - Q&A

Phenix Workshop 11/17/2020 (Xtallography) - Q&A Phenix Tutorials

318 views - 5 years ago

Phenix Workshop 11/17/2020 (Xtallography) - Top tips for molecular replacement

Phenix Workshop 11/17/2020 (Xtallography) - Top tips for molecular replacement Phenix Tutorials

5.6K views - 5 years ago

Phenix Workshop 11/17/2020 (Xtallography) - Experimental Phasing and model building

Phenix Workshop 11/17/2020 (Xtallography) - Experimental Phasing and model building Phenix Tutorials

1.6K views - 5 years ago

Phenix User Workshop 9/15/2020 - Introduction to Phenix

Phenix User Workshop 9/15/2020 - Introduction to Phenix Phenix Tutorials

1.4K views - 5 years ago

Phenix User Workshop 9/15/2020 - Cryo-EM map improvement

Phenix User Workshop 9/15/2020 - Cryo-EM map improvement Phenix Tutorials

4.7K views - 5 years ago

Phenix User Workshop 9/15/2020 - Automated model building

Phenix User Workshop 9/15/2020 - Automated model building Phenix Tutorials

1.4K views - 5 years ago

Phenix User Workshop 9/15/2020 - Q/A sesseion

Phenix User Workshop 9/15/2020 - Q/A sesseion Phenix Tutorials

255 views - 5 years ago

Phenix User Workshop 9/16/2020 - phenix.real_space_refine

Phenix User Workshop 9/16/2020 - phenix.real_space_refine Phenix Tutorials

1.1K views - 5 years ago

Phenix User Workshop 9/16/2020 - Ligands in refinement

Phenix User Workshop 9/16/2020 - Ligands in refinement Phenix Tutorials

2K views - 5 years ago

Phenix User Workshop 9/16/2020 - Validation

Phenix User Workshop 9/16/2020 - Validation Phenix Tutorials

596 views - 5 years ago

Phenix User Workshop 9/16/2020 - Q&A

Phenix User Workshop 9/16/2020 - Q&A Phenix Tutorials

223 views - 5 years ago

Density modification for cryo-EM maps

Density modification for cryo-EM maps Phenix Tutorials

5.2K views - 6 years ago

How to run real-space-refine

How to run real-space-refine Phenix Tutorials

11.9K views - 7 years ago

How to use secondary structure restraints

How to use secondary structure restraints Phenix Tutorials

3.6K views - 7 years ago

How to use multiple refinement strategies and apply them to selected parts of a model

How to use multiple refinement strategies and apply them to selected parts of a model Phenix Tutorials

3.3K views - 7 years ago

Simulate a SAD experiment with phenix.plan_sad_experiment

Simulate a SAD experiment with phenix.plan_sad_experiment Phenix Tutorials

1.6K views - 8 years ago

Automatic map interpretation with map_to_model

Automatic map interpretation with map_to_model Phenix Tutorials

9.5K views - 8 years ago

Scaling and merging anomalous data

Scaling and merging anomalous data Phenix Tutorials

1.9K views - 8 years ago

Automated map sharpening with phenix.autosharpen

Automated map sharpening with phenix.autosharpen Phenix Tutorials

5.8K views - 8 years ago

Fitting ligands into density with phenix.ligandfit

Fitting ligands into density with phenix.ligandfit Phenix Tutorials

6.3K views - 8 years ago

Advanced Tutorial phenix.xtriage - Space Group Identification, Ice rings & Wilson Plot

Advanced Tutorial phenix.xtriage - Space Group Identification, Ice rings & Wilson Plot Phenix Tutorials

2.8K views - 8 years ago

Advanced Tutorial phenix.xtriage - Checking for twinning

Advanced Tutorial phenix.xtriage - Checking for twinning Phenix Tutorials

2.3K views - 8 years ago

Advanced Tutorial phenix.xtriage - translational NCS (tNCS)

Advanced Tutorial phenix.xtriage - translational NCS (tNCS) Phenix Tutorials

4.1K views - 8 years ago

Checking data quality with phenix.xtriage

Checking data quality with phenix.xtriage Phenix Tutorials

3.8K views - 8 years ago

Automated model building with Phenix AutoBuild

Automated model building with Phenix AutoBuild Phenix Tutorials

6.2K views - 8 years ago

Mini-lecture: Density modification

Mini-lecture: Density modification Phenix Tutorials

2.3K views - 8 years ago

SAD phasing using AutoSol

SAD phasing using AutoSol Phenix Tutorials

4.4K views - 8 years ago

Introduction to interactive low-resolution model building with ISOLDE

Introduction to interactive low-resolution model building with ISOLDE Phenix Tutorials

9.7K views - 8 years ago

MolProbity: All atom contacts tutorial

MolProbity: All atom contacts tutorial Phenix Tutorials

2.4K views - 8 years ago

How to run MolProbity (web interface and Phenix GUI)

How to run MolProbity (web interface and Phenix GUI) Phenix Tutorials

6K views - 8 years ago

Overview of cryo-EM tools in Phenix

Overview of cryo-EM tools in Phenix Phenix Tutorials

7.2K views - 8 years ago

How to run Structure Comparison

How to run Structure Comparison Phenix Tutorials

2.8K views - 8 years ago