本文主要介绍了在Linux平台下安装开源版Pymol的简单方法。由于官方主要提供商业版本的安装方法，只有Windows系统下的编译包才能提供whl安装包平台。事实上，在Anaconda库中有一个开源版本的pymol。顺便说一句，借这篇文章来推广它。
技术背景PyMol是一种类似VMD的分子可视化工具，也是在PyQT的基础上开发的。但由于其商业运营，软件分为三个版本：教育版、开源版和商业版。教育版会有水印，商业版会收费，但官方不会提供开源版的安装方法。根据参考链接1的内容，可以在Windows系统上安装开源版Pymol，但发行版只有Windows平台的编译包。因此，如果需要在Linux上安装PyMol，只能在Github上下载源码进行编译和构建。
然而，经过几次尝试，在编译过程中会遇到很多问题，尤其是在手动构建netcdf时，这些问题总是表明它们无法构建。经过多个平台的搜索，我们最终发现anaconda的库中有一个名为pymol-open-source详见参考链接2。这个包是PyMol的开源版，但是在网上很难找到这个包的相关信息。它不仅是开源版，而且几乎支持整个平台的使用。本文主要简要介绍了包的安装和简单使用。
直接执行本地conda环境下的下列指令，即可自动完成安装：
$ conda install -c conda-forge pymol-open-sourceCollecting package metadata (current_repodata.json): doneSolving environment: done==> WARNING: A newer version of conda exists. <== current version: 23.1.0 latest version: 23.5.0Please update conda by running $ conda update -n base -c defaults condaOr to minimize the number of packages updated during conda update use conda install conda=23.5.0## Package Plan ## environment location: /home/dechin/Anaconda3//envs/mindsponge added / updated specs: - pymol-open-sourceThe following packages will be downloaded: package | build ---------------------------|----------------- glm-0.9.9.8 | h00ab1b0_0 213 KB conda-forge hdf5-1.12.2 |nompi_h4df4325_101 3.2 MB conda-forge libnetcdf-4.8.1 |nompi_h21705cb_104 1.5 MB conda-forge pymol-open-source-2.5.0 | py39hc95a48e 6.8 MB conda-forge xorg-libxau-1.0.11 | hd590300_0 14 KB conda-forge ------------------------------------------------------------ Total: 11.7 MBThe following NEW packages will be INSTALLED: c-ares conda-forge/linux-64::c-ares-1.19.1-hd590300_0 curl conda-forge/linux-64::curl-8.1.2-h409715c_0 dbus anaconda/pkgs/main/linux-64::dbus-1.13.18-hb2f20db_00 expat conda-forge/linux-64::expat-2.5.0-hcb278e6_1 fontconfig conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_ gettext conda-forge/linux-64::gettext-0.21.1-h2707fc_ glew conda-forge/linux-64::glew-2.1.0-h9c3ff4c_2 glib conda-forge/linux-64::glib-2.76.3-hfc55251_000 glib-tools conda-forge/linux-64::glib-tools-2.76.3-hfc55251_000 glm conda-forge/linux-64::glm-0.9.9.8-h00ab1b0 gst-plugins-base anaconda/pkgs/main/linux-64::gst-plugins-base-1.14.1-h6a678d_ gstreamer anaconda/pkgs/main/linux-64::gstreamer-1.14.1-h5eee18b_ hdf4 conda-forge/linux-64::hdf4-4.2.15-h9772cbc_5 hdf5 conda-forge/linux-64::hdf5-1.12.2-nompi_h4df4325_101 icu conda-forge/linux-64::icu-58.2-hf44d3e_10000 keyutils conda-forge/linux-64::keyutils-1.6.-h166bdaf_00 krb5 conda-forge/linux-64::krb5-1.20.1-h81ceb04 libaec conda-forge/linux-64::libaec-1.0.6-hcb278e6_1 libclang anaconda/pkgs/main/linux-64::libclang-10.0.1-default_hb85057a_2 libcurl conda-forge/linux-64::libcurl-8.1.2-h409715c_0 libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 libev conda-forge/linux-64::libev-4.33-h516909a_1 libevent conda-forge/linux-64::libevent-2.1.12-hf998b51_1 libexpat conda-forge/linux-64::libexpat-2.5.0-hcb278e6_1 libglib conda-forge/linux-64::libglib-2.76.3-hebfc3b9_00 libglu conda-forge/linux-64::libglu-9.0.0-hac7e632_1002 libiconv conda-forge/linux-64::libiconv-1.17-h16bdaf_00 libllvm10 conda-forge/linux-64::liblvm10-10.0.1-he513fc3_3 libnetcdf conda-forge/linux-64::libnetcdf-4.8.1-nompi_h21705cb_104 libnghttp2 conda-forge/linux-64::libnghttp2-1.52.0-h61bc06f_00 libpq anaconda/pkgs/main/linux-64::libpq-12.15-hdbd6064_ libsh2 conda-forge/linux-64::libsh2-1.11.0-h0841786_0 libxcb conda-forge/linux-64::libxcb-1.15-h0b41bf4_00 libxkbcommon anaconda/pkgs/main/linux-64::libxkbcommon-1.0.1-hfa300c1_0 libxml2 anaconda/pkgs/main/linux-64::libxml2-9.9.14-h74e7548_0 libxslt anaconda/pkgs/main/linux-64::libxslt-1.1.35-h4e12654_0 libzip conda-forge/linux-64::libzip-1.9.2-hc929e4a_1 nspr conda-forge/linux-64::nspr-4.35-h27087fc_0 nss conda-forge/linux-64::nss-3.89-he45b914_0 pcre2 conda-forge/linux-64::pcre2-10.40-hc3806b_00 ply conda-forge/noarch::ply-3.11-py_1 pmw conda-forge/linux-64::pmw-2.0.1-py39hf3d152e_ pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1000 pymol-open-source conda-forge/linux-64::pymol-open-source-2.5.py39hc95a48e pyqt anaconda/pkgs/main/linux-64::pyqt-5.15.7-py39h6a678d_ pyqt5-sip anaconda/pkgs/main/linux-64::pyqt5-sip-12.11.0-py39h6a678d_ qt-main anaconda/pkgs/main/linux-64::qt-main-5.15.2-h327a75a_7 qt-webengine anaconda/pkgs/main/linux-64::qt-webengine-5.15.9-hd2092_4 qtwebkit anaconda/pkgs/main/linux-64::qtwebkit-5.212-h4eab89a_4 sip conda-forge/linux-64::sip-6.6.2-py39h5a03fae_00 sqlite anaconda/pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_ toml conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0 xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002 xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.6-h8ee46fc_00 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.11-hd590300_0 xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0 xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h0b41bf4_2 xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h0b41bf4_1003 xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007 The following packages will be SUPERSEDED by a higher-priority channel: ca-certificates anaconda/pkgs/main::ca-certificates-2~ --> conda-forge::ca-certificates-2023.5.7-hbcca054_00 certifi anaconda/pkgs/main/linux-64::certifi-~ --> conda-forge/noarch::certifi-2023.5.7-pyhd8ed1ab_0 Proceed ([y]/n)? yDownloading and Extracting Packages Preparing transaction: done Verifying transaction: done Executing transaction: done安装完成后，直接输入终端命令行窗口pymol您可以打开Pymol界面。点击File->Open导入pdb文件等相关分子构象输入文件，如下图所示，是导入pdb文件后的效果图。
本文主要介绍了在Linux平台下安装开源版Pymol的简单方法。由于官方主要提供商业版本的安装方法，只有Windows系统下的编译包才能提供whl安装包平台。事实上，在Anaconda库中有一个开源版本的pymol。顺便说一句，借这篇文章来推广它。
版权声明作者ID：DechinPhy
腾讯云专栏同步：https://cloud.tencent.com/developer/column/91958
51CTO同步链接：https://blog.51cto.com/u_15561675
参考链接- https://anaconda.org/conda-forge/pymol-open-source
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