四、在af中使用pymol（一）conda下的pymol安装和创建桌面图标

2023-05-05 00:09:37 admin 34

（一）conda下的pymol安装

1、linux下的安装

配置环境
source /appsnew/source/Anaconda3-2022.05-local.sh
创建虚拟环境
conda create -n yourpymol2.5
激活虚拟环境
conda activate yourpymol2.5
注意，我们在系统里使用了 alphafold2.3的虚拟环境，所以后面使用conda activate alphafold2.3，里面含有pymol2.5
安装pymol2.5版本
conda install -c schrodinger -c conda-forge pymol或安装pymol2.4等版本
conda install -c schrodinger pymol-bundle
退出虚拟环境：
conda  deactivate
conda  deactivate
第一次退出yourpymol2.5；第二次退出 Anaconda3

原文：https://pymol.org/conda/

PyMOL 2.5 and later

(Updated August 20, 2021)

Since PyMOL 2.5, our pymol conda packages are based on conda-forge. The following command will install PyMOL on Windows, macOS or Linux into a conda environment:

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

macOS Specifics

On macOS, you need this command in addition:

pip install PyQt5

Previous versions

For PyMOL 2.0 to 2.4, this command should be sufficient:

conda install -c schrodinger pymol

2、安装桌面图标

1）激活环境

[chen@login29 ~]# source /appsnew/source/Anaconda3-2022.05-local.sh
(base)[chen@login29 ~]$conda activate pymol2.5
(pymol2.5)

2）查找pymol 图标文件

(base)[chen@login29 ~]$conda activate pymol2.5 
(pymol2.5) which pymol
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/bin/pymol
(pymol2.5) find  /appsnew/usr/python/Anaconda3-local/envs/pymol2.5/  -iname *png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/lib/tk8.6/demos/images/earthmenu.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/lib/tk8.6/demos/images/ouster.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/lib/python3.8/idlelib/Icons/idle_16.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/lib/python3.8/idlelib/Icons/idle_256.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/lib/python3.8/idlelib/Icons/idle_32.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/lib/python3.8/idlelib/Icons/idle_48.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/share/pymol/data/openvr/hints_vive_controller.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/share/pymol/data/openvr/menu_splash.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/share/pymol/data/pymol/icons/icon2_128x128.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/share/pymol/data/pymol/icons/icon2_16x16.png
/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/share/pymol/data/pymol/icons/icon2_32x32.png

3）将上面查找的结果，填入红色字体部分

chen@login29 ~]# vi ~/桌面/pymol2.5.desktop

[Desktop Entry]
Type=Application
GenericName=pymol
Comment=ThunderbirdMail:The Language of Technical Computing
Exec=/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/bin/pymol
Icon=/appsnew/usr/python/Anaconda3-local/envs/pymol2.5/share/pymol/data/pymol/icons/icon2_128x128.png
Terminal=false
Categories=GNOME;GTK;Graphics;Scanning;
Name=pymol
Name[zh_CN.UTF-8]=pymol结构软件