Pymol获取蛋白表面残基

1. 获取AAV衣壳蛋白组装体的结构
   pymol中使用命令:

set assembly, 1    # 设置加载模式为组装体
# set assembly, ""   # 设置加载模式为单体
fetch 3ux1, assembly1, async=0    # 从PDB下载结构

2. 下载FindSurfaceResidues脚本
   从FindSurfaceResidues - PyMOLWiki
   下载FindSurfaceResidues python脚本
   使用命令:

run /path/to/findSurfaceResidues.py
findSurfaceResidues doShow=1, cutoff=2.5

findSurfaceResidues 使用方法:

findSurfaceResidues [ selection=all [, cutoff=2.5 [, doShow=0 ]]]

参数：

• selection = str: The object or selection for which to find exposed residues {default: all}
• cutoff = float: The cutoff in square Angstroms that defines exposed or not. Those atoms with > cutoff Ang^2 exposed will be considered exposed {default: 2.5 Ang^2}
• doShow = 0/1: Change the visualization to highlight the exposed residues vs interior {default: 0}