We can all agree that typing commands into PyMOL can make pretty and publishable pictures. But your love for PyMOL lasts until you realise there is a mistake and need to re-do it. Or have to iterate over several proteins. And it takes many fiddly commands to get yourself back there (relatable rant over). Recently I was introduced to the useful tool of PML scripting, and for those who have not already discovered this gem please do read on.

These scripts can be called when you launch PyMOL (or from File>Run) and iterate through the commands in the script to adapt the image. This means all your commands can be adjusted to make the figure optimal and allow for later editing.

I have constructed and commented an example script (Joe_Example.pml) below to give a basic depiction of a T4 Lysozyme protein. Here I load the structure and set the view (the co-ordinates can be copied from PyMOL easily by clicking the ‘get view’ command). You then essentially call the commands that you would normally use to enhance your image. To try this for yourself, download the T4 Lysozyme structure from the PBD (1LYD) and running the script (command line: pymol Joe_Example.pml) in the same directory to give the image below.

The image generated by the attached PML script of the T4 Lysozyme (PDB: 1LYD)

#########################
### Load your protein ###
#########################

load ./1lyd.pdb, 1lyd

##########################
### Set your viewpoint ###
##########################

set_view (\
    -0.682980239,    0.305771887,   -0.663358808,\
    -0.392205656,    0.612626553,    0.686194837,\
     0.616211832,    0.728826880,   -0.298486710,\
     0.000000000,    0.000000000, -155.216171265,\
     4.803394318,   63.977561951,  106.548652649,\
   123.988197327,  186.444198608,   20.000000000 )

#################
### Set Style ###
#################

hide everything
set cartoon_fancy_helices = 1
set cartoon_highlight_color = grey70
bg_colour white
set antialias = 1
set ortho = 1
set sphere_mode, 5

############################
### Make your selections ###
############################

select sampleA, 1lyd and resi 1-20

colour blue, 1lyd
colour red, sampleA
show cartoon, 1lyd


###################
### Save a copy ###
###################

ray 1000,1500
png Lysozyme_Example_Output.png

Enjoy!