One 、Snapshot（ Different colors show different secondary structures of proteins , Show different small molecules in different colors , Display hyphen ）

load name.pdb,name

#>fetch object

#>disable object-name

#>enable object-name

#>delete selection-name

#>show representation # among representation It can be for ：cartoon, ribbon, dots, spheres, surface and mesh

#>hide representation

#>as representation

as follows ：

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 # Show the small molecule as a bat model

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 # Show the distance between atoms ： perhaps wizard-measurement

hide labels

Two 、 load namd Dynamic trajectory ：

First of all, will dcd For documents cpptraj Turn into mdcrd file , And then again pymol Run command in

Loading track ：

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 # Calculate the secondary structure

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

3、 ... and 、 Animation

Define animation

mset 1 x30

mdo Command to create a swing +/-180 Degree 30 Frame animation

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 # Record a text document , The file should have a suffix of .pml

Pymol> log_close # Termination record

Pymol> @script-file-name # Call the document

external GUI Inside the window File － Save Session, Create a session file （.pse）, Next time you open it Pymol Directly return to the current state .

Pymol> png file-name # The picture is saved in PyMOL Install in the default folder

pymol> fetch 1w2i # Load a pdb molecular

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*

Next, measure the distance ,Wizard -> Measurement -> Distance, Make a little beautification , hold cartoon After adjusting the transparency of , You can get the following figure ：