Pymol里常用到的命令，随用随记

python脚本运行方式：

1, File->Run Script->选择python脚本;

2, run python脚本

常用命令：

load *.pdb

remove solvent

select str1, resn Cl-

remove str1

align WT_ligs, WT_box_wat_eq3 #后面的是target

alignto WT_ligs #把所有pdb都align到WT_ligs

show sticks, resi 87

set label_size, -1.4

set label_color, black, selection

select selection, resid 84+85+86+94+98+101+151+273+274+278+282+285+336+341+342+345+346+348+418+421+422+423+425+426+430

png image.png, 10cm, dpi=300, ray=1

png image.png, width=3000, height=2400, dpi=300, ray=1

高精度做图命令：

hide

hide labels, agi

show sticks, lig | res  #棒状显示lig和res对象，"|"为逻辑“或”

select 5A， byres ligand around 5 #选取ligand5A范围内残基

hide sticks, h.  #隐藏H原子

zoom lig | res  #居中放大lig和res，其他对象虚化

color wheat, lig & name C*  #将lig的碳原子（以C开头的原子名）设为小麦色

set label_size, 30

set label_font_id, 9

#########

import center_of_mass

select AGI1, resn AGI & name C2+C3+C4+C5+C6

com AGI1, object=p1

select AGI2, resn AGI & name C7+C8+C9+C10+C11

com AGI2, object=p2

hide everything, p*

show spheres, p*

hide labels, measure*

set dash_length, 0.3

set dash_radius, 0.08

set dash_gap, 0.3

color green, measure01

color gray70, measure02

bg_color white

show cartoon

#########

color smudge, lig & name C*

set cartoon_transparency, 0.3

set cartoon_round_helices, 1

set cartoon_fancy_helices, 1

set cartoon_fancy_sheets, 1

set cartoon_color, green, FLS_TPP_DHA & chain A  #设置不同链的cartoon不同颜色

set stick_ball #显示棍棒模型

set stick_ball_ratio, 1.8

unset opaque_background   # 设置背景透明，只在ray下有用

#########

save focus.pse

png label.png

hide labels

png focus.png, 16.93cm, 16.93cm, dpi=300, ray=1

zoom

set cartoon_transparency, 0

png overview.png, 20cm, 18cm, dpi=300, ray=1

save overview.pse