在Linux上安装和使用免费版本的PyMol

技术背景

PyMol是一个类似于VMD的分子可视化工具，也是在PyQt的基础上开发的。但是由于其商业化运营，软件分为了教育版、开源版和商业版三个版本。其中教育版会有水印，商业版要收费，但是官方不提供开源版本的安装方法。按照参考链接1的内容，可以在Windows系统上面安装一个开源版本的PyMol，但是该发行版只有Windows平台的编译包。所以如果需要在Linux上安装PyMol，就只能在Github上面下载源码进行编译构建。

但是经过数番尝试，在编译过程中会遇到不少问题，尤其是在手动构建netcdf的时候，总是提示无法构建。在经过多个平台的检索之后，最终发现在Anaconda的库中有一个名为pymol-open-source的包，详情可见参考链接2。这个包就是PyMol的开源版本，但是网上几乎很难找到这个包的相关信息。它不仅仅是开源版，还几乎支持了全平台的使用，本文主要简单介绍一下这个包的安装和简单使用。

安装pymol-open-source

在本地的conda环境下，直接执行如下指令，即可自动完成安装：

$ conda install -c conda-forge pymol-open-source
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 23.1.0
  latest version: 23.5.0

Please update conda by running

    $ conda update -n base -c defaults conda

Or 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-source


The 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         6.8 MB  conda-forge
    xorg-libxau-1.0.11         |       hd590300_0          14 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        11.7 MB

The 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_0 
  expat              conda-forge/linux-64::expat-2.5.0-hcb278e6_1 
  fontconfig         conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0 
  gettext            conda-forge/linux-64::gettext-0.21.1-h27087fc_0 
  glew               conda-forge/linux-64::glew-2.1.0-h9c3ff4c_2 
  glib               conda-forge/linux-64::glib-2.76.3-hfc55251_0 
  glib-tools         conda-forge/linux-64::glib-tools-2.76.3-hfc55251_0 
  glm                conda-forge/linux-64::glm-0.9.9.8-h00ab1b0_0 
  gst-plugins-base   anaconda/pkgs/main/linux-64::gst-plugins-base-1.14.1-h6a678d5_1 
  gstreamer          anaconda/pkgs/main/linux-64::gstreamer-1.14.1-h5eee18b_1 
  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-hf484d3e_1000 
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 
  krb5               conda-forge/linux-64::krb5-1.20.1-h81ceb04_0 
  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_0 
  libglu             conda-forge/linux-64::libglu-9.0.0-hac7e632_1002 
  libiconv           conda-forge/linux-64::libiconv-1.17-h166bdaf_0 
  libllvm10          conda-forge/linux-64::libllvm10-10.0.1-he513fc3_3 
  libnetcdf          conda-forge/linux-64::libnetcdf-4.8.1-nompi_h21705cb_104 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.52.0-h61bc06f_0 
  libpq              anaconda/pkgs/main/linux-64::libpq-12.15-hdbd6064_1 
  libssh2            conda-forge/linux-64::libssh2-1.11.0-h0841786_0 
  libxcb             conda-forge/linux-64::libxcb-1.15-h0b41bf4_0 
  libxkbcommon       anaconda/pkgs/main/linux-64::libxkbcommon-1.0.1-hfa300c1_0 
  libxml2            anaconda/pkgs/main/linux-64::libxml2-2.9.14-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-hc3806b6_0 
  ply                conda-forge/noarch::ply-3.11-py_1 
  pmw                conda-forge/linux-64::pmw-2.0.1-py39hf3d152e_1007 
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001 
  pymol-open-source  conda-forge/linux-64::pymol-open-source-2.5.0-py39hc95a48e_6 
  pyqt               anaconda/pkgs/main/linux-64::pyqt-5.15.7-py39h6a678d5_1 
  pyqt5-sip          anaconda/pkgs/main/linux-64::pyqt5-sip-12.11.0-py39h6a678d5_1 
  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-hd2b0992_4 
  qtwebkit           anaconda/pkgs/main/linux-64::qtwebkit-5.212-h4eab89a_4 
  sip                conda-forge/linux-64::sip-6.6.2-py39h5a03fae_0 
  sqlite             anaconda/pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0 
  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_0 
  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_0 
  certifi            anaconda/pkgs/main/linux-64::certifi-~ --> conda-forge/noarch::certifi-2023.5.7-pyhd8ed1ab_0 


Proceed ([y]/n)? y


Downloading and Extracting Packages
                                                                                  
Preparing transaction: done                                                       
Verifying transaction: done                                                       
Executing transaction: done

安装完成后，直接在终端命令行窗口输入pymol即可打开PyMol的界面。我们可以点击File->Open来导入相关的分子构象输入文件，比如pdb文件等，如下所示是一个导入pdb文件后的效果图。