Install the open source version of PyMOL on Linux
This article is not complete, please browse the last part to confirm whether this article is what you need!
Open source philosophy
In recent years, the various embargo threats to teak are obvious to all. The masons next door (HIT students call themselves "workers", then I would call them "Masons") are not able to use MATLAB to participate in the competition. Therefore, this article installs the open source version of PyMOL (to make a clear distinction from the commercial version and the cracked version).
What is this article
This article is a checklist tutorial for installing the open source version of PyMOL under Linux.
What this article is not
This article is still not a women's dress tutorial.
Introduction to PyMOL
PyMOL is a protein visualization software launched by the famous computer-aided drug design developer Schrödinger. As a commercial software, PyMOL is divided into open source, educational, and commercial versions. Because the Schrödinger company is also going to have a meal, the open source version is slightly limited in function. The relationship between the open source and commercial versions of PyMOL is similar to the relationship between Visual Studio Code and Visual Studio.
Create environment
Due to the conflicts between PyMOL and chempy and other packages, if you install too many conflicting packages in the default environment, it is tantamount to raising Gu. Therefore, create a virtual environment called "pymol" so that PyMOL is isolated from the Anaconda basic environment.
source ~/anaconda3/bin/activate root
# 启动Anaconda默认环境
conda create -n pymol
# 创建pymol环境
conda activate pymol
# 启动pymol环境
It is recommended to enter the code line by line, and do not close the Terminal after completion, and use it in the next step.
Install PyMOL wheels and dependencies
We complete the installation of PyMOL and the required numpy, mkl, and pmw packages in a virtual environment.
Unknown reasons cause pip to not deploy normally, so first install pip, then install numpy, mkl, pmw.
conda install pip
pip install numpy mkl pmw -i https://pypi.tuna.tsinghua.edu.cn/simple
Obviously, the evil capitalist Schrödinger company will not let you easily get the open source version of PyMOL software. although
The University of California, Irvine provides built open source wheels , but the provided whl file is only applicable to Windows systems (I stepped on the pit here). So we need to compile from scratch.
Hope you read here before reading
At this point, I found that relevant content is not what I am good at. Moreover, PyMOL is the last step of the experimental process. Is it not good to complete the related work under the Windows system? Have to torture yourself to use Ubuntu. So this article ends here, if readers still try to compile from scratch, the following information is enough for you to complete the relevant steps:
CentOS installation process of free and open source PyMOL
Free open source version of PyMOL installation
The installation .whl file appears is not a supported wheel on this platform.