# 初始化
reinitialize
# 设置背景颜色(白色)
set bg_rgb, white
# 设置渲染出图时的背景为透明背景
set ray_opaque_background, 1
# 设置以surface显示时的显示质量，数字越大，质量越高，但是加载时间更长
set surface_quality, 1
# load命令加载指定的文件进入pymol中
load g10577_dip.pdb
load g10577_swiss_tetra.pdb
# set_name修改进入pymol的object的名字，可以改的简短一些，方便写脚本的时候使用
set_name g10577_dip, dip
set_name g10577_swiss_tetra, tetra
# align命令，将tetra结构，align到dip上，dip不懂，tetra在动
align tetra, dip
# 接下来时展示环节，先把屏幕上的东西都隐藏掉，之后按需显示
hide
# 把所有的object都以cartoon的形式展示
as cartoon
# 为两个结构上色，因为绝大部分结构都一模一样，所以就都先用一样的颜色，之后用其他颜色突出突变位点
color green, dip
color green, tetra
# 把两个蛋白上面发生了突变的位点选择中，并且放到一个集合中，方便之后一同管理操作
select unique_dip, (dip and resi 120,184,200,202,208,750,765,769,778,858,914,920,956,1173,1195)
select unique_tetra, (tetra and resi 120,184,200,202,208,750,765,769,778,858,914,920,956,1173,1195)
# 根据查到的信息，把两个蛋白上面被注释的位点也选择起来
select c2h2, resi 253-268
select preintegrase, resi 437-483
select transposase, resi 502-611
select transcriptase, resi 863-1106
select RNaseHI, resi 1190-1347
select bindingsite, (resi 1194-1197,1232-1234,1237,1271,1297,1324)
# 为刚才选择起来的集合进行上色
color pink, c2h2
color tv_yellow, preintegrase
color tv_orange, transposase
color wheat, transcriptase
color cyan, RNaseHI
color magenta, bindingsite
color red, unique_dip
color marine, unique_tetra
# 把两个蛋白上突变位点的残基以sticks形式展示，可以更为直观看到侧链的变化
show sticks, unique_dip
show sticks, unique_tetra
# 展示侧链的时候会显示每一个原子，默认所有原子都是一个颜色的，使用下面这个命令，可以按照原子种类上色
color atomic, (not elem C)
# 在pymol界面调整好想要记录下来的视角之后，get_view拷贝下来这个视角所对应的坐标数据，下次要转到这个视角的时候，直接把下面set_view的坐标数据粘贴进去就好了
set_view (\
-0.443876743, -0.887108207, -0.126545846,\
0.379024029, -0.313832849, 0.870543838,\
-0.811979711, 0.338450551, 0.475540578,\
-0.000006333, 0.000010125, -378.091735840,\
2.868264437, 8.263483047, 3.565798283,\
-1093.241333008, 1849.422973633, -20.000000000 )
# 输入更为清晰的图片，分辨率为5120x2880
ray 5120,2880
# 把渲染好的图片保存为png，名字是full-cartoon, dpi一般设置为600
png full-cartoon, dpi=600
set_view (\
0.162854165, 0.761085987, -0.627874792,\
0.986317217, -0.141892508, 0.083828166,\
-0.025284013, -0.632946193, -0.773780227,\
-0.000447951, 0.000333518, -174.528823853,\
18.261980057, 1.092945337, -65.594757080,\
135.276504517, 213.771804810, -20.000000000 )
ray 5120,2880
png mutantsloop-cartoon, dpi=600
set_view (\
-0.797870755, -0.220254272, -0.561154008,\
-0.347436249, -0.592696846, 0.726631165,\
-0.492635280, 0.774724066, 0.396375328,\
0.000064261, -0.000044622, -102.471977234,\
19.247808456, 10.199863434, 26.562820435,\
81.191818237, 123.754402161, -20.000000000 )
ray 5120,2880
png mutantshelix1-cartoon, dpi=600
set_view (\
-0.351793468, -0.932474613, 0.082071237,\
0.506030798, -0.115682706, 0.854718089,\
-0.787508488, 0.342217654, 0.512558758,\
-0.000131886, 0.000076436, -95.525459290,\
-14.267536163, 25.109249115, 1.946354866,\
57.438381195, 133.602249146, -20.000001907 )
ray 5120,2880
png mutantshelix2-cartoon, dpi=600
set_view (\
0.483249426, -0.873959482, 0.051630318,\
0.254665822, 0.083903082, -0.963376462,\
0.837620437, 0.478705883, 0.263115048,\
0.000054307, 0.000128813, -90.844551086,\
-18.277912140, -17.079923630, 12.054067612,\
78.273773193, 103.398162842, -20.000001907 )
ray 5120,2880
png mutantshelix3-cartoon, dpi=600
# 这两个命令需要安装psico的插件之后才可以使用，否则要显示表面电势就只能鼠标操作plugin-apbs
apbs_surface dip
apbs_surface tetra
set_view (\
-0.386296988, -0.921947718, -0.028120210,\
0.183486909, -0.106687434, 0.977212012,\
-0.903937221, 0.372336805, 0.210379750,\
0.000000000, 0.000000000, -450.677978516,\
17.319509506, -11.700004578, -10.965003967,\
347.316009521, 554.039916992, -20.000000000 )
ray 5120,2880
png dip_apbs, dpi=600
ray 5120,2880
png tetra_apbs, dpi=600