蛋白设计之软件安装

1. Pymol
   地址：·https://pymol.org/·

conda install -c conda-forge -c schrodinger pymol-bundle
····
**`https://pymolwiki.org/index.php/Main_Page`
使用说明；**

2. ChimeraX
   地址：·https://www.cgl.ucsf.edu/chimerax/download.html·
   ·ChimeraX is the state-of-the-art visualization program from the Resource for Biocomputing, Visualization, and Informatics at UC San Francisco. It is free for academic, government, nonprofit, and personal use; commercial users, please see commercial licensing. Please cite ChimeraX in publications.·

https://www.cgl.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py
https://www.cgl.ucsf.edu/chimerax/tutorials.html

3. gmxMMPBSA
   下载参照教程

https://www.zhihu.com/people/swing-78-25/posts

4. rosetta

wget https://www.rosettacommons.org/downloads/academic/3.14/rosetta_bin_li
 nux_3.14_bundle.tar.bz2

进⼊到下载⽂件的⽂件夹，解压⽂件，这⼀步也要⼏⼩时。

tar -xvjf rosetta_bin_linux_3.14_bundle.tar.bz2

解压完毕后，设置环境变量

vim ~/.bashrc 1
shift+G到达文件最低端2
键入i进入编辑模式


export ROSETTA=/home/your_name/software/rosetta.binary.linux.release-371
export ROSETTA3_DB=$ROSETTA/main/database
export ROSETTA_BIN=$ROSETTA/main/source/bin
export PATH=$PATH:$ROSETTA_BIN
export LD_LIBRARY_PATH=$ROSETTA/main/source/bin:$LD_LIBRARY_PATH
第⼀⾏⾥改成⾃⼰的⽂件路径

在命令⾏中输⼊rosetta后连按两次Tab键，返回多个rosetta程序说明安装成功。

5. RIF

https://github.com/rifdock/rifdock

下载安装

conda create --name rifdock
wget https://www.rosettacommons.org/downloads/academic/3.9/rosetta_bin_linux_3.9_bundle.tgz
tar -xzvf rosetta_bin_linux_3.9_bundle.tgz

mkdir -p ~/miniconda3/envs/rifdock/etc/conda/activate.d
vim ~/miniconda3/envs/rifdock/etc/conda/activate.d/rosetta.sh

rosetta.sh中写

#!/bin/bash
 # Backup old environment variables
 export OLD_ROSETTA=$ROSETTA
 export OLD_ROSETTA3_DB=$ROSETTA3_DB
 export OLD_ROSETTA_BIN=$ROSETTA_BIN
 export OLD_PATH=$PATH
 export OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
 # Set up new environment variables for Rosetta
 export ROSETTA="/home/your_name/software/rosetta.binary.linux.release-371"
 export ROSETTA3_DB="$ROSETTA/main/database"
 export ROSETTA_BIN="$ROSETTA/main/source/bin"
 export PATH="$PATH:$ROSETTA_BIN"
 export LD_LIBRARY_PATH="$ROSETTA/main/source/bin:$LD_LIBRARY_PATH"
 

设置退出环境时的脚本：

dir -p ~/miniconda3/envs/rifdock/etc/conda/deactivate.d
vim ~/miniconda3/envs/rifdock/etc/conda/deactivate.d/rosetta_deactivate.sh

rosetta_deactivate.sh中写：

#!/bin/bash
 # Restore original environment variables
 export ROSETTA=$OLD_ROSETTA
 export ROSETTA3_DB=$OLD_ROSETTA3_DB
 export ROSETTA_BIN=$OLD_ROSETTA_BIN
 export PATH=$OLD_PATH
 export LD_LIBRARY_PATH=$OLD_LD_LIBRARY_PATH
 # Unset old environment variables
 unset OLD_ROSETTA
 unset OLD_ROSETTA3_DB
 unset OLD_ROSETTA_BIN
 unset OLD_PATH
 unset OLD_LD_LIBRARY_PATH

chmod +x ~/miniconda3/envs/rifdock/etc/conda/activate.d/rosetta_activate.sh
chmod +x ~/miniconda3/envs/rifdock/etc/conda/deactivate.d/rosetta_deactivate.sh

在激活rifdock环境后，输⼊

 echo $ROSETTA

会返回3.9版本。
接下来按照附件中ubuntu_rifdock_compilation_extra.pdf安装后续软件