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Phenix Documentation
<?xml version="1.0" encoding="utf-8" ?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Phenix Documentation</title> <link rel="stylesheet" type="text/css" href="css/html4css1.css" /> <link rel="stylesheet" type="text/css" href="css/stylesheet.css" /> </head> <body> <div id="header"> <a href="index.html"> <img src="icons/phenix-logo-small.jpg" alt="PHENIX" height="20%" width="20%" /> <span> <strong>P</strong>ython-based <strong>H</strong>ierarchical <strong>EN</strong>vironment for <strong>I</strong>ntegrated <strong>X</strong>tallography </span> </a> </div> <!-- This will be placed inside template.html as html_body --> <div class="wide"> <h3>Phenix Documentation - version 1.21.2-5419</h3> <table style="width:90%"> <tr> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a href="overviews/xray_index.html"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <img style="width: 120px;" src="./images/xray.png" alt="xray image"> </center> </div> <div class="indexcard-topimage_title"> <center class=CardTitle> Crystallography </center> </div> </a> </div> </td> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a href="overviews/cryo-em_index.html"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <img style="width: 120px;" src="./images/cryoem_grayscale.png" alt="xray image"> </center> </div> <div class="indexcard-topimage_title"> <center class=CardTitle> Cryo-EM </center> </div> </a> </div> </td> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a href="overviews/predicted_models_index.html"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <img style="width: 100px;" src="./images/aa_grayscale.png" alt="xray image"> </center> </div> <div class="indexcard-topimage_title" > <center class=CardTitle> Predicted models </center> </div> </a> </div> </td> </tr> <tr> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a href="install-setup-run.html"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <svg xmlns="http://www.w3.org/2000/svg" width="90" height="90" fill="currentColor" class="bi bi-folder-check" viewBox="0 0 16 16"> <path d="m.5 3 .04.87a1.99 1.99 0 0 0-.342 1.311l.637 7A2 2 0 0 0 2.826 14H9v-1H2.826a1 1 0 0 1-.995-.91l-.637-7A1 1 0 0 1 2.19 4h11.62a1 1 0 0 1 .996 1.09L14.54 8h1.005l.256-2.819A2 2 0 0 0 13.81 3H9.828a2 2 0 0 1-1.414-.586l-.828-.828A2 2 0 0 0 6.172 1H2.5a2 2 0 0 0-2 2zm5.672-1a1 1 0 0 1 .707.293L7.586 3H2.19c-.24 0-.47.042-.683.12L1.5 2.98a1 1 0 0 1 1-.98h3.672z"/> <path d="M15.854 10.146a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.707 0l-1.5-1.5a.5.5 0 0 1 .707-.708l1.146 1.147 2.646-2.647a.5.5 0 0 1 .708 0z"/> </svg> <!-- or this one: https://icons.getbootstrap.com/icons/gear/ --> <!-- <svg xmlns="http://www.w3.org/2000/svg" width="90" height="90" fill="currentColor" class="bi bi-tools" viewBox="0 0 16 16"> <path d="M1 0 0 1l2.2 3.081a1 1 0 0 0 .815.419h.07a1 1 0 0 1 .708.293l2.675 2.675-2.617 2.654A3.003 3.003 0 0 0 0 13a3 3 0 1 0 5.878-.851l2.654-2.617.968.968-.305.914a1 1 0 0 0 .242 1.023l3.27 3.27a.997.997 0 0 0 1.414 0l1.586-1.586a.997.997 0 0 0 0-1.414l-3.27-3.27a1 1 0 0 0-1.023-.242L10.5 9.5l-.96-.96 2.68-2.643A3.005 3.005 0 0 0 16 3c0-.269-.035-.53-.102-.777l-2.14 2.141L12 4l-.364-1.757L13.777.102a3 3 0 0 0-3.675 3.68L7.462 6.46 4.793 3.793a1 1 0 0 1-.293-.707v-.071a1 1 0 0 0-.419-.814L1 0Zm9.646 10.646a.5.5 0 0 1 .708 0l2.914 2.915a.5.5 0 0 1-.707.707l-2.915-2.914a.5.5 0 0 1 0-.708ZM3 11l.471.242.529.026.287.445.445.287.026.529L5 13l-.242.471-.026.529-.445.287-.287.445-.529.026L3 15l-.471-.242L2 14.732l-.287-.445L1.268 14l-.026-.529L1 13l.242-.471.026-.529.445-.287.287-.445.529-.026L3 11Z"/> </svg> --> </center> </div> <div class="indexcard-topimage_title"> <center class=CardTitle> How to install </center> </div> </a> </div> </td> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a href="phenix_gui.html"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <svg xmlns="http://www.w3.org/2000/svg" width="90" height="90" fill="currentColor" class="bi bi-hand-index" viewBox="0 0 16 16"> <path d="M6.75 1a.75.75 0 0 1 .75.75V8a.5.5 0 0 0 1 0V5.467l.086-.004c.317-.012.637-.008.816.027.134.027.294.096.448.182.077.042.15.147.15.314V8a.5.5 0 1 0 1 0V6.435a4.9 4.9 0 0 1 .106-.01c.316-.024.584-.01.708.04.118.046.3.207.486.43.081.096.15.19.2.259V8.5a.5.5 0 0 0 1 0v-1h.342a1 1 0 0 1 .995 1.1l-.271 2.715a2.5 2.5 0 0 1-.317.991l-1.395 2.442a.5.5 0 0 1-.434.252H6.035a.5.5 0 0 1-.416-.223l-1.433-2.15a1.5 1.5 0 0 1-.243-.666l-.345-3.105a.5.5 0 0 1 .399-.546L5 8.11V9a.5.5 0 0 0 1 0V1.75A.75.75 0 0 1 6.75 1zM8.5 4.466V1.75a1.75 1.75 0 1 0-3.5 0v5.34l-1.2.24a1.5 1.5 0 0 0-1.196 1.636l.345 3.106a2.5 2.5 0 0 0 .405 1.11l1.433 2.15A1.5 1.5 0 0 0 6.035 16h6.385a1.5 1.5 0 0 0 1.302-.756l1.395-2.441a3.5 3.5 0 0 0 .444-1.389l.271-2.715a2 2 0 0 0-1.99-2.199h-.581a5.114 5.114 0 0 0-.195-.248c-.191-.229-.51-.568-.88-.716-.364-.146-.846-.132-1.158-.108l-.132.012a1.26 1.26 0 0 0-.56-.642 2.632 2.632 0 0 0-.738-.288c-.31-.062-.739-.058-1.05-.046l-.048.002zm2.094 2.025z"/> </svg> </center> </div> <div class="indexcard-topimage_title"> <center class=CardTitle> GUI introduction </center> </div> </a> </div> </td> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a href="faqs/index.html"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <svg xmlns="http://www.w3.org/2000/svg" width="90" height="90" fill="currentColor" class="bi bi-patch-question" viewBox="0 0 16 16"> <path d="M8.05 9.6c.336 0 .504-.24.554-.627.04-.534.198-.815.847-1.26.673-.475 1.049-1.09 1.049-1.986 0-1.325-.92-2.227-2.262-2.227-1.02 0-1.792.492-2.1 1.29A1.71 1.71 0 0 0 6 5.48c0 .393.203.64.545.64.272 0 .455-.147.564-.51.158-.592.525-.915 1.074-.915.61 0 1.03.446 1.03 1.084 0 .563-.208.885-.822 1.325-.619.433-.926.914-.926 1.64v.111c0 .428.208.745.585.745z"/> <path d="m10.273 2.513-.921-.944.715-.698.622.637.89-.011a2.89 2.89 0 0 1 2.924 2.924l-.01.89.636.622a2.89 2.89 0 0 1 0 4.134l-.637.622.011.89a2.89 2.89 0 0 1-2.924 2.924l-.89-.01-.622.636a2.89 2.89 0 0 1-4.134 0l-.622-.637-.89.011a2.89 2.89 0 0 1-2.924-2.924l.01-.89-.636-.622a2.89 2.89 0 0 1 0-4.134l.637-.622-.011-.89a2.89 2.89 0 0 1 2.924-2.924l.89.01.622-.636a2.89 2.89 0 0 1 4.134 0l-.715.698a1.89 1.89 0 0 0-2.704 0l-.92.944-1.32-.016a1.89 1.89 0 0 0-1.911 1.912l.016 1.318-.944.921a1.89 1.89 0 0 0 0 2.704l.944.92-.016 1.32a1.89 1.89 0 0 0 1.912 1.911l1.318-.016.921.944a1.89 1.89 0 0 0 2.704 0l.92-.944 1.32.016a1.89 1.89 0 0 0 1.911-1.912l-.016-1.318.944-.921a1.89 1.89 0 0 0 0-2.704l-.944-.92.016-1.32a1.89 1.89 0 0 0-1.912-1.911l-1.318.016z"/> <path d="M7.001 11a1 1 0 1 1 2 0 1 1 0 0 1-2 0z"/> </svg> </center> </div> <div class="indexcard-topimage_title" > <center class=CardTitle> FAQs </center> </div> </a> </div> </td> </tr> <tr> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a class="reference external" href="https://www.youtube.com/c/phenixtutorials"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <svg xmlns="http://www.w3.org/2000/svg" width="90" height="90" fill="currentColor" class="bi bi-camera-video" viewBox="0 0 16 16"> <path fill-rule="evenodd" d="M0 5a2 2 0 0 1 2-2h7.5a2 2 0 0 1 1.983 1.738l3.11-1.382A1 1 0 0 1 16 4.269v7.462a1 1 0 0 1-1.406.913l-3.111-1.382A2 2 0 0 1 9.5 13H2a2 2 0 0 1-2-2V5zm11.5 5.175 3.5 1.556V4.269l-3.5 1.556v4.35zM2 4a1 1 0 0 0-1 1v6a1 1 0 0 0 1 1h7.5a1 1 0 0 0 1-1V5a1 1 0 0 0-1-1H2z"/> </svg> </center> </div> <div class="indexcard-topimage_title"> <center class=CardTitle> Video tutorials </center> </div> </a> </div> </td> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a href="tutorials.html"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <svg xmlns="http://www.w3.org/2000/svg" width="90" height="90" fill="currentColor" class="bi bi-chat-text" viewBox="0 0 16 16"> <path d="M2.678 11.894a1 1 0 0 1 .287.801 10.97 10.97 0 0 1-.398 2c1.395-.323 2.247-.697 2.634-.893a1 1 0 0 1 .71-.074A8.06 8.06 0 0 0 8 14c3.996 0 7-2.807 7-6 0-3.192-3.004-6-7-6S1 4.808 1 8c0 1.468.617 2.83 1.678 3.894zm-.493 3.905a21.682 21.682 0 0 1-.713.129c-.2.032-.352-.176-.273-.362a9.68 9.68 0 0 0 .244-.637l.003-.01c.248-.72.45-1.548.524-2.319C.743 11.37 0 9.76 0 8c0-3.866 3.582-7 8-7s8 3.134 8 7-3.582 7-8 7a9.06 9.06 0 0 1-2.347-.306c-.52.263-1.639.742-3.468 1.105z"/> <path d="M4 5.5a.5.5 0 0 1 .5-.5h7a.5.5 0 0 1 0 1h-7a.5.5 0 0 1-.5-.5zM4 8a.5.5 0 0 1 .5-.5h7a.5.5 0 0 1 0 1h-7A.5.5 0 0 1 4 8zm0 2.5a.5.5 0 0 1 .5-.5h4a.5.5 0 0 1 0 1h-4a.5.5 0 0 1-.5-.5z"/> </svg> </center> </div> <div class="indexcard-topimage_title"> <center style="font-size: 12pt;"> Tutorials & Examples </center> </div> </a> </div> </td> <td> <div class="indexcard indexcard-topimage" style="width:240px"> <a href="reference/index.html"> <div class="indexcard-topimage_header" style="background-color:#e0e0eb; width:200px"> <center> <svg xmlns="http://www.w3.org/2000/svg" width="90" height="90" fill="currentColor" class="bi bi-body-text" viewBox="0 0 16 16"> <path fill-rule="evenodd" d="M0 .5A.5.5 0 0 1 .5 0h4a.5.5 0 0 1 0 1h-4A.5.5 0 0 1 0 .5Zm0 2A.5.5 0 0 1 .5 2h7a.5.5 0 0 1 0 1h-7a.5.5 0 0 1-.5-.5Zm9 0a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5Zm-9 2A.5.5 0 0 1 .5 4h3a.5.5 0 0 1 0 1h-3a.5.5 0 0 1-.5-.5Zm5 0a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5Zm7 0a.5.5 0 0 1 .5-.5h3a.5.5 0 0 1 0 1h-3a.5.5 0 0 1-.5-.5Zm-12 2A.5.5 0 0 1 .5 6h6a.5.5 0 0 1 0 1h-6a.5.5 0 0 1-.5-.5Zm8 0a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5Zm-8 2A.5.5 0 0 1 .5 8h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5Zm7 0a.5.5 0 0 1 .5-.5h7a.5.5 0 0 1 0 1h-7a.5.5 0 0 1-.5-.5Zm-7 2a.5.5 0 0 1 .5-.5h8a.5.5 0 0 1 0 1h-8a.5.5 0 0 1-.5-.5Zm0 2a.5.5 0 0 1 .5-.5h4a.5.5 0 0 1 0 1h-4a.5.5 0 0 1-.5-.5Zm0 2a.5.5 0 0 1 .5-.5h2a.5.5 0 0 1 0 1h-2a.5.5 0 0 1-.5-.5Z"/> </svg> </center> </div> <div class="indexcard-topimage_title" > <center style="font-size: 12pt;"> Overview of programs </center> </div> </a> </div> </td> </tr> </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. Bunk贸czi, 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> <a href="reference/dock_predicted_model.html">Dock processed predicted model in cryo-EM map</a><br> <a href="reference/dock_and_rebuild.html">Process, dock and rebuild predicted model in cryo-EM map</a><br> <a href="reference/trim_overlapping.html">Trim parts of one model overlapping another</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"> <area shape="rect" coords="213,15,363,69" href="overviews/xray-experimental-phasing.html" alt="Experimental phasing" 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"> <area shape="rect" coords="422,212,574,240" href="overviews/xray-refinement.html" alt="Structure refinement" title="Optimize an atomic model with respect to the experimental data and prior chemical knowledge"> <area shape="rect" coords="421,238,573,266" href="overviews/validation.html" alt="Structure validation" title="Validate a structure with respect to prior chemical knowledge"> <area shape="rect" coords="207,212,368,264" href="overviews/ligands.html" alt="Ligands" 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>--> <!-- Image Map Generated by http://www.image-map.net/ --> <!-- <map name="cryoemoverview"> <area target="" alt="Auto-sharpen map" title="Auto-sharpen map" href="overviews/cryo-em-map-manipulations.html" coords="8,57,170,114" shape="rect"> <area target="" alt="Dock a model into a cryo-EM map" title="Dock a model into a cryo-EM map" href="overviews/cryo-em-dock-model.html" coords="206,15,389,73" shape="rect"> <area target="" alt="Autobuild a model into a cryo-EM map" title="Autobuild a model into a cryo-EM map" href="overviews/cryo-em-model-building.html" coords="208,89,389,147" shape="rect"> <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/auto_sharpen.html">Auto-sharpen a map</a> | <a href="reference/local_resolution.html">Calculate a local resolution map</a> | <a href="reference/local_aniso_sharpen.html">Optimize a map with local anisotropic 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> --> </div> </body> </html>