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phenix_documentation.html
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<!-- This will be placed inside template.html as html_body -->
<div class="wide">
<h3>Phenix Documentation - version INSTALLED_VERSION</h3>
<table style="width:90%">
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<td>
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Crystallography
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Cryo-EM
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Predicted models
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How to install
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GUI introduction
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FAQs
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<tr>
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<div class="indexcard indexcard-topimage" style="width:240px">
<a class="reference external" href="https://www.youtube.com/c/phenixtutorials">
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Video tutorials
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Tutorials & Examples
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Overview of programs
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</table>
<br>
<h2>Other links</h2>
<a href="reference/citations.html">Bibliography</a><br>
<a href="dictionary.html">Dictionary</a><br>
<a href="phenix_index.html">Index</a><br>
<a href="reference/find_program.html">Find a program or regression test</a><br>
<br>
<br>
<h2>Citing Phenix</h2>
<p>If you use PHENIX please cite:</p>
<p><b>Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.</b> D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkóczi, V. B. Chen, T. I. Croll, B. Hintze, L.-W. Hung, S. Jain, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, B. K. Poon, M. G. Prisant, R. J. Read, J. S. Richardson, D. C. Richardson, M. D. Sammito, O. V. Sobolev, D. H. Stockwell, T. C. Terwilliger, A. G. Urzhumtsev, L. L. Videau, C. J. Williams and P. D. Adams. Acta Cryst. (2019). D75, 861-877</p>
<!--
<blockquote>
<a href="reference/tutorial_channel.html">Video tutorials</a><br>
<a href="phenix_programs.html">Phenix programs and their functions</a><br>
<a href="phenix_gui.html">Running Phenix with the graphical interface</a><br>
<a href="tutorials.html">Tutorials and Examples</a><br>
<a href="dictionary.html">Dictionary of crystallographic and other terms<a><br>
<a href="faqs/index.html">FAQs: Frequently asked questions</a><br>
<a href="install-setup-run.html">How to install, setup and run Phenix</a><br>
<a href="reference/index.html">Complete Phenix reference documentation</a><br>
<a href="reference/find_program.html">Find a program or regression test</a><br>
<a href="reference/citations.html">Bibliography</a><br>
<a href="phenix_index.html">Index</a><br>
</blockquote>
<h3>Working with AlphaFold2, RoseTTAFold and other predicted models</h3>
<blockquote>
<a href="reference/alphafold.html">AlphaFold and Phenix</a><br>
<a href="reference/predict_and_build.html">Solve X-ray structure or interpret cryo-EM map with iterative prediction and rebuilding</a><br>
<a href="reference/predict_model.html">Model prediction with AlphaFold</a><br>
<a href="reference/process_predicted_model.html">Process predicted model</a><br>
</blockquote>
<h3>Crystallographic Structure Solution with Phenix</B></h3>
<blockquote><img height="280" src="images/xtal-overview-map.001.jpg" usemap="#xrayoverview"></blockquote>
<map name="xrayoverview">
<area shape="rect" coords="4,48,154,102" href="overviews/xray-data-quality.html" alt="Data Quality"
title="Check data for pathologies and suitability for structure solution">
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title="Solve the phase problem using anomalous or isomorphous differences">
<area shape="rect" coords="213,82,363,136" href="overviews/xray-molecular-replacement.html" alt="Molecular replacement"
title="Solve the phase problem using known molecular structures">
<area shape="rect" coords="423,48,573,102" href="overviews/density-modification.html" alt="Density Modification"
title="Improve phases using density modificaton methods">
<area shape="rect" coords="423,130,573,184" href="overviews/xray-model-building.html" alt="Model building"
title="Automatically build an atomic model into an electron density map">
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title="Optimize an atomic model with respect to the experimental data and prior chemical knowledge">
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title="Validate a structure with respect to prior chemical knowledge">
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title="Fit and/or identify ligands and create stereochemical restraints">
<area shape="rect" coords="627,211,778,265" href="overviews/xray-structure-deposition.html" alt="Structure Deposition"
title="Deposit model and data at the world wide Protein Data Bank">
</map>
<blockquote><U><B>Phenix Documentation for X-ray Crystallography</B></U></blockquote>
<blockquote>
<a href="reference/xtriage_gui.html">Checking data quality</a> |
<a href="reference/autosol_gui.html">Experimental phasing</a> |
<a href="reference/phaser_mr.html">Molecular replacement</a> |
<a href="reference/autobuild_gui.html">Model building</a> |
<a href="reference/refine_gui.html">Structure refinement</a><br>
<a href="reference/validation.html">Structure validation</a> |
<a href="reference/ligandfit_gui.html">Ligand fitting</a> |
<a href="making_geometry_restraints.html">Making geometry restraints</a> |
<a href="overviews/xray-structure-deposition.html">Structure deposition</a>|
<a href="reference/index.html">All</a><br>
</blockquote>
<h3>Phenix Documentation for Neutron Crystallography</h3>
<blockquote>
<a href="reference/refine_gui.html">Structure refinement</a> |
<a href="reference/validation.html">Structure validation</a> |
<a href="making_geometry_restraints.html">Making geometry restraints</a> |
<a href="overviews/xray-structure-deposition.html">Structure deposition</a>|
<a href="reference/index.html">All</a><br>
</blockquote>
<h3>Cryo-EM Structure Solution with Phenix</h3>
<blockquote><img height="220" src="images/cryoem-overview-map.001.jpg" usemap="#cryoemoverview"></blockquote>-->
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<area target="" alt="Optimize an atomic model with respect to the map and prior chemical knowledge"
title="Optimize an atomic model with respect to the map and prior chemical knowledge" href="overviews/cryo-em-real-space-refinement.html"
coords="433,52,601,110" shape="rect">
<area target="" alt="Validate data and a structure with respect to prior chemical knowledge"
title="Validate data and a structure with respect to prior chemical knowledge" href="overviews/cryo-em-validation.html"
coords="433,154,601,209" shape="rect">
<area target="" alt="Deposit model and data at the world wide Protein Data Bank"
title="Deposit model and data at the world wide Protein Data Bank" href="overviews/cryo-em-structure-deposition.html"
coords="637,154,780,209" shape="rect">
</map>
<blockquote><U><B>Phenix Documentation for Electron Microscopy (EM)</B></U></blockquote>
<blockquote>
<a href="overviews/cryo-em-map-quality.html">Map quality assessment</a> |
<a href="overviews/cryo-em-map-symmetry.html">Map symmetry</a> |
<a href="reference/real_space_refine.html">Structure refinement</a> |
<a href="reference/mtriage.html">Map statistics (resolution, etc)</a> |
<a href="reference/local_resolution.html">Calculate a local resolution map</a> |
<a href="reference/map_sharpening.html">Optimize a map with sharpening</a> |
<a href="reference/resolve_cryo_em.html">Density modify a map</a> |
<a href="reference/dock_in_map.html">Dock a model into a map</a> |
<a href="reference/em_placement.html">Likelihood-based model docking into a cryo-EM map</a> |
<a href="reference/emplace_local.html">Dock a model into a local volume</a> |
<a href="reference/trace_and_build.html">Rapid model-building</a> |
<a href="reference/sequence_from_map.html">Guess sequences from map</a> |
<a href="reference/cryo_fit.html">Flexibly fit a model to a map</a> |
<a href="reference/map_to_model.html">Build a model</a> |
<a href="making_geometry_restraints.html">Making geometry restraints</a> |
<a href="reference/chain_comparison.html">Compare CA/P in two models</a> |
<a href="reference/map_symmetry.html">Identify symmetry in a map</a> |
<a href="reference/combine_focused_maps.html">Combine best parts of focused maps</a> |
<a href="reference/map_box.html">Extract box with map and model</a> |
<a href="reference/map_to_structure_factors.html">Convert map to structure factors</a> |
<a href="reference/segment_and_split_map.html">Segment a map</a> |
<a href="reference/refine_ca_model.html">Adjust a CA/CB model</a> |
<a href="reference/fix_insertions_deletions.html">Fix register errors</a> |
<a href="reference/douse.html">Build ordered water</a> |
<a href="reference/index.html">All</a><br>
</blockquote>
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</div>