20230307 Mac M1 install open-source pymol-安装开源版本pymol

正常情况下 : brew install pymol

运行以下命令即可

brew install pymol 

实际会遇到的问题：下载错误

许多包都难以下载成功，报以下错误

url: (92) HTTP/2 stream 0 was not closed cleanly: PROTOCOL_ERROR (err 1)

Error: pymol: Failed to download resource "python@3.11"
Download failed: https://www.python.org/ftp/python/3.11.2/Python-3.11.2.tgz

解决：修改hosts文件，追加DNS

即使修改了hosts，也会下载失败，多下载几次可以成功

vim /etc/hosts

185.199.108.133 raw.githubusercontent.com
151.101.1.63    pythonhosted.org
151.101.1.168   python.org

ip可以在https://www.ipaddress.com 查询

启动

在控制台中输入pymol即可启动

其他参考方式

brew安装开源和dmg安装程序，然后替换dmg安装文件夹中启动项

https://blog.csdn.net/weixin_45725149/article/details/123698134

1. 安装官网的dmg文件
2. 编译github source
3. 覆盖：编译好的pymol覆盖dmg安装文件下的pymol

编译

# MacPorts
sudo port install pymol
 
# Homebrew
brew install brewsci/bio/pymol

覆盖

which pymol
# <where-is-pymol>
sudo cp <where-is-pymol> /Applications/PyMOL.app/Contents/MacOS

覆盖失败

# error
cp: /Applications/PyMOL.app/Contents/MacOS/pymol: Operation not permitted

删掉dmg

brew install pymol 

成功，缺陷就是只能从控制台启动pymol

conda安装

https://zhuanlan.zhihu.com/p/514911704

conda install -c conda-forge -c schrodinger pymol-bundle

报错，找不到包

(base) xx@xx ~ % conda install -c conda-forge -c schrodinger pymol-bundle
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - pymol-bundle

Current channels:

  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/osx-arm64
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
  - https://conda.anaconda.org/schrodinger/osx-arm64
  - https://conda.anaconda.org/schrodinger/noarch
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/osx-arm64
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/osx-arm64
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/noarch
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/osx-arm64
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

  - https://conda.anaconda.org/schrodinger/osx-arm64
  - https://conda.anaconda.org/schrodinger/noarch

换成国内镜像应该可行
并且怀疑从这个schrodinger源安装的pymol-bundle可能是收费的

其他问题：

• 安装anaconda，然后在这个环境中，许多包都难以安装成功，修改镜像之后也难成功，总是装成x86的包，然后导致包冲突。
• 解决：安装mambaforge，更早支持了Apple M1芯片，使用默认源即可安装许多包
• 参考： 一文解释 conda,pip,anaconda,miniconda,miniforge

下一步计划

学习pymol的使用，可视化相互作用界面
安装插件，减少重复工作

• paper：Shortcuts for faster image creation in PyMOL
• Code： https://github.com/MooersLab/pymolshortcuts