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：
代码语言：javascript复制$ 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。
总结概要
这篇文章主要介绍在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的安装方法，而提供whl安装包的平台也只有Windows系统下的编译包。其实在Anaconda的库中是有提供pymol的开源版本的，这里借这篇文章顺便推广一下。
版权声明
本文首发链接为：https://cloud.tencent.com/developer/article/2300994
作者ID：DechinPhy
更多原著文章请参考：https://www.cnblogs.com/dechinphy/
打赏专用链接：https://www.cnblogs.com/dechinphy/gallery/image/379634.html
腾讯云专栏同步：https://cloud.tencent.com/developer/column/91958
CSDN同步链接：https://blog.csdn.net/baidu_37157624?spm=1008.2028.3001.5343
51CTO同步链接：https://blog.51cto.com/u_15561675
参考链接
- https://blog.csdn.net/MurphyStar/article/details/106904126
- https://anaconda.org/conda-forge/pymol-open-source
