pymol-note

Posted 2022-04-08 jszd

一、Snapshot（用不同颜色显示蛋白不同二级结构，用不同颜色显示不同小分子，显示连键）

>load name.pdb,name

#>fetch object

#>disable object-name

#>enable object-name

#>delete selection-name

#>show representation  #其中representation可以为：cartoon, ribbon, dots, spheres, surface和mesh

#>hide representation

#>as representation

如下：

>load last.pdb,2fkw

>hide all

>show cartoon,2fkw

>dss 2fkw

>color red,ss h

>color yellow,ss s

>color blue,ss “”

> set cartoon_transparency, 0.5

>select bcl,resn BCL

>show sticks,bcl

>color green,bcl

>select rg1,resn RG1

>show sticks,rg1

>color orange,rg1

>set stick_radius,0.15   #将小分子显示为球棍模型

>set sphere_scale, 0.2

>show spheres, bcl

>show spheres, rg1

>select mg,name MG

>color pink,mg

>alter mg,vdw=2

>rebuild

>wizard measurement  #显示原子之间距离：或者wizard-measurement

>hide labels

二、加载namd动力学轨迹：

首先将dcd文件用cpptraj转化为mdcrd文件，然后再pymol中运行命令

加载轨迹：

>load prmtop,mmm,format=top

>load_traj 02_Heat.mdcrd,mmm,format=trj, start=1, stop=10001, interval=100

>hide

>show cartoon,mmm

>dss mmm   #计算二级结构

> color red,ss h

> color blue,ss l+

> color yellow,ss s

>select THM,selection

>color yellow,THM

>show sticks,THM

>bg_color white

>ray 900,900

 

三、动画

# 定义动画

mset 1 x30

# mdo命令创建摇摆+/-180度的30帧动画

util.mrock start, finish, angle, phase, loop-flag

util.mrock 1,30,180,1,1

mplay

>bg_color white

>ray

>save test.png

**********

pymol>zoom all

>color red,all

> hide

> dss 1kim

> show cartoon,1kim

> color red,ss h

> color blue,ss l+

> color yellow,ss s

>select THM,selection

>color yellow,THM

>show sticks,THM

>bg_color white

>ray 900,900

Cited from: http://www.sohu.com/a/218617791_777125

 

Pymol> log_open script-file-name.pml #记录一个文本文档，该文件的后缀名应为.pml

Pymol> log_close # 终止记录

Pymol> @script-file-name # 调用该文档

外部GUI窗口里面的File － Save Session，创建一个会话文件（.pse），下次打开Pymol时直接回到当前所在的状态。

Pymol> png file-name # 图片被保存在PyMOL安装默认的文件夹中

pymol> fetch 1w2i  # 载入一个pdb分子

Hide everything and then show protein cartoon

• PyMOL> hide everything, all

• PyMOL> show cartoon, all

Color the helix, sheet, and loop

• PyMOL> color purple, ss h

• PyMOL> color yellow, ss s

• PyMOL> color green, ss ""

Color chain A and B

• PyMOL> color red, chain A

• PyMOL> color blue, chain B

Color the active site residue

PyMOL> select active, (resi 14-20,38 and chain A)

PyMOL> color yellow, active

PyMOL> turn y, -60; turn x, -20

PyMOL> zoom active

Locate and display the bound formate ion in the active site.

PyMOL> select ligand, active around 3.5 and resn FMT

PyMOL> show sticks, ligand

PyMOL> show spheres, ligand

PyMOL> alter ligand, vdw=0.5

PyMOL> rebuild

PyMOL> set transparency=0.25

8Rendering and output

• PyMOL> bg_color white

• PyMOL> ray

• File -> Save Image

 

Display the side-chain of active site residues on top of the cartoon representation

• PyMOL> hide surface

• PyMOL> select sidechain, not (name c+n+o)

• PyMOL> show sticks, (active and sidechain)

• PyMOL> color blue, name n*

• PyMOL> color red, name o*

• PyMOL> color white, name c*

接下来进行距离的衡量，Wizard -> Measurement -> Distance，进行稍微的美化，把cartoon的透明度调整后，即可得到下图：