{"id":11033,"date":"2024-03-06T16:15:25","date_gmt":"2024-03-06T16:15:25","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=11033"},"modified":"2024-03-06T16:18:21","modified_gmt":"2024-03-06T16:18:21","slug":"open-source-pymol-installation-on-windows","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2024\/03\/open-source-pymol-installation-on-windows\/","title":{"rendered":"Open Source PyMOL installation on Windows"},"content":{"rendered":"\n<p>A year ago, I used Gheorghe Rotaru&#8217;s helpful <a href=\"https:\/\/www.blopig.com\/blog\/2022\/03\/how-to-install-open-source-pymol-on-windows-10\/\">blog post<\/a> to install PyMOL. Unfortunately, after resetting my computer, I have just discovered that some of the links are broken. Here are the installation steps with new links provided by <a href=\"https:\/\/github.com\/cgohlke\">Christoph Gohlke<\/a>, who generously offers pre-compiled Windows versions of the latest PyMOL software along with all its requirements.<\/p>\n\n\n\n<p><strong>Install the latest version of Python 3 for Windows:<\/strong><br>Download the Windows Installer (x-bit) for Python 3 from their\u00a0<a href=\"https:\/\/www.python.org\/downloads\/windows\/\" target=\"_blank\" rel=\"noreferrer noopener\">website<\/a>, with x being your Windows architecture \u2013 32 or 64.<br><br>Follow\u00a0<a href=\"https:\/\/docs.python.org\/3\/using\/windows.html#the-full-installer\" target=\"_blank\" rel=\"noreferrer noopener\">the instructions<\/a>\u00a0provided on how to install Python. You can confirm the installation by running &#8216;py&#8217; in PowerShell.<\/p>\n\n\n\n<!--more-->\n\n\n\n<p><strong>Download all required wheel files:<\/strong><br>You need to download the wheels of Numpy and Pymol.<br>For <a href=\"https:\/\/github.com\/cgohlke\/numpy-mkl-wheels\/releases\">numpy<\/a>,  download the latest numpy+mkl files corresponding to the Python version you have installed and the one matching your Windows architecture. For example, for Python 3.12 on a 64-bit Windows, download the <br>numpy-1.26.3-cp312-cp312-win_amd64.whl&nbsp;file.<br><br>Similarly, for <a href=\"https:\/\/github.com\/cgohlke\/pymol-open-source-wheels\/releases\">Pymol<\/a>, download the PyMOL launcher and PyMOL itself. Ensure that they match your Python version and Windows architecture.<\/p>\n\n\n\n<p><strong>Install requirements and PyMOL from wheels:<\/strong><br>Open a Windows PowerShell instance and change to the directory containing all the .whl files (using the cd command).<br>Install numpy and PyMOL from the wheels using the following command in PowerShell or&nbsp;<a href=\"https:\/\/pip.pypa.io\/en\/latest\/user_guide\/#installing-from-wheels\" target=\"_blank\" rel=\"noreferrer noopener\">follow these instructions:<\/a><\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>py -m pip install wheel_file.whl<\/code><\/pre>\n\n\n\n<p>You should install them in this order:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Numpy<\/li>\n\n\n\n<li>PyMOL<\/li>\n\n\n\n<li>PyMOL launcher<\/li>\n<\/ul>\n\n\n\n<p><strong>Launch PyMOL:<\/strong><br><br>Now that PyMOL is installed, you can open the PyMOL app by typing the following command in PowerShell:<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>py.exe -m pymol<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>A year ago, I used Gheorghe Rotaru&#8217;s helpful blog post to install PyMOL. Unfortunately, after resetting my computer, I have just discovered that some of the links are broken. Here are the installation steps with new links provided by Christoph Gohlke, who generously offers pre-compiled Windows versions of the latest PyMOL software along with all [&hellip;]<\/p>\n","protected":false},"author":110,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[14,351,221],"tags":[],"ppma_author":[750],"class_list":["post-11033","post","type-post","status-publish","format-standard","hentry","category-howto","category-molecular-visualization","category-python"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":750,"user_id":110,"is_guest":0,"slug":"yael","display_name":"Yael Ziv","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/3c9bc72679de72f6dcf8e4c545102ef6e0cf449a772414f2a7958c9c1971b740?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/11033","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/110"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=11033"}],"version-history":[{"count":5,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/11033\/revisions"}],"predecessor-version":[{"id":11052,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/11033\/revisions\/11052"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=11033"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=11033"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=11033"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=11033"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}