Pymol常用命令

http://pymol.chenzhaoqiang.com/intro/overview.html

选择命令

select resn HIS 按照残基名称选择

alter (chain D), resv += 223 修改残基编号，依次顺移223位

help + 命令帮助文档

alter name, chain ="A" 加链的信息

select all

create sele, com 合成一个PDB

select idx. +原子序数

select name +原子名称

寻找蛋白1qox互作界面（chainI和J）的残基

interfaceResidues("1qox", cA="c. I", cB="c. J", cutoff=0.75, selName="foundIn1QOX")

脚本批量叠合算重原子的RMSD

from pymol import cmd
import pandas as pd
rmsd_df = pd.DataFrame(columns=["name","rmsd"],index=[i for i in range(1,76)])
cmd.load("ranked_1_0.pdb")
cmd.create('ali1','resi 1-125 and ranked_1_0')
inde = 1
for i in range(1,16):
        for j in range(5):
                name = "ranked_" + str(i) + "_" + str(j) + ".pdb"
                cmd.load(name)
                selection="resi 1-125 and " + "ranked_" + str(i) + "_" + str(j)
                cmd.create('ali2',selection)
                a = cmd.align('ali1 and name CA+C+N+O','ali2 and name CA+C+N+O')[0]
                rmsd_df.loc[inde,"rmsd"] = str(a)[:5]
                rmsd_df.loc[inde,"name"] = "ranked_" + str(i) + "_" + str(j)
                inde += 1
                cmd.delete('ali2')
rmsd_df.to_csv("rmsd.csv",index=False,encoding='utf-8')