# general_comments.pml
# --------------------
# A PyMOL script input file with comments.
# This file includes the most useful PyMOL options for many image types.
# Lines that start with a hash (#) are comments
# Some commands are commented out as well, uncomment if needed.
# ";" separates commands, we use it here to place the comments after the
command for explanations
# Text file without comments here.
# This file to save as pml file with comments here.
reinitialize ; #reinitialize
PyMOL to startup state -> important especially for re-reading pml
scripts
# load structures
# ---------------
# load one or several structures
# load ../my_pdb.pdb, pdb1
fetch 4eiy, pdb1 ; # fetches structure file from PDB entry
4eiy (as cif file)
# load ../my_reference.pdb, pdb2
# superpositions: use "super" or "cealign" instead of "align" for proteins
with seq_identity <~ 30 %; align moved, reference
# align pdb1 and name CA, pdb2 and name CA and resi 100-200 ; #
align based on CA coordinates and a certain region of the structure.
# create objects or selections
# ----------------------------
create ligand, pdb1 and chain A and resi 2401
create receptor, pdb and chain A and not residue 2401
create env, byres (resn ZMA around 5.0) and not resn ZMA ; # all
residues 5 Ang. around the ligand
# select ligenv, ligand or env
# general definitions and graphics
# --------------------------------
# note that the fog, fog_start, opaque_background options also change the
corresponding options for ray trace mode, but these can also be controlled
individually
#viewport 800, 600 ; # size of Pymol screen
-> should be adapted to match the approx. visual appearance of the
objects you want to show
set hash_max, 100 ; # memory assigned for
ray tracing (in MB). Default is 100. Increase for increased speed,
decrease if PyMOL crashes upon ray tracing
set bg_rgb, white ; # white background. set
bg can be used with predefined Pymol color values.
(https://pymolwiki.org/index.php/Color_Values)
set depth_cue, on ; # Enable fog in openGL
rendering (draw and interactive view)
set fog, 1.0
; # Sets fog density (0.0 ... 1.0)
set fog_start, 0.6 ; # controls z depth, where
fog starts. Decrease to start more in front.
set orthoscopic, on ; # Turning orthoscopic on, turns
perspective off, -> parallel lines: parallel, identical for close and
distant objects
clip slab, 100 ; # Sets
the slab thickness to value in Angstrom, centered at the current screen
center
set opaque_background, on ; # Draw background in bg_rgb color. Set
to "off" for transparent background.
set ray_shadows, off ; # Do not generate shadows in ray
tracing mode
hide everything ; # hide all
previous objects, e.g. default PyMOL representations upon loading
structures
# fold cartoon
# ------------
dss ; # improved secondary structure assignment
# set cartoon_side_chain_helper, on ; # for residues represented
in cartoon and sticks: show only side_chain, force cartoon to go through
CA
# set cartoon_fancy_helices, on ; # test on and off and see
what you prefer
# set cartoon_highlight_color, white ; # color on the inside of
helices
set cartoon_gap_cutoff, 20; # increase the distance cutoff up to
which missing loops will be shown as broken lines
set cartoon_transparency, 0.0 ; # set cartoon transparency from 0.0
... 1.0, may be followed by selection
show cartoon, receptor
# set cartoon_color, paleblue, receptor; # set the cartoon color
independent of CA color (default is: CA color)
# molecular
surface
# -----------------
#create msurface, receptor ; # create a new object for the surface to
be able to switch it on and off
#hide all, msurface
#show surface, msurface
#set transparency, 0.5 , msurface; # transparency is in fact the cartoon
transparency
#set surface_color, white, msurface ; # otherwise the color of the atoms
near the surface will determine the color of the nearby surface regions
# residues
#----------
set stick_radius, 0.2
set valence, 0 ; # valence > 0 shows double
bonds as such
#show sticks, resi 101-103 and chain A ; # show this residue range
#show sticks, resn CYS and (sidechain or name CA) ; # show all
cysteine side chains
#show sticks, env
show sticks, resi 100+200 and not name C+N+O ; # show only side
chain for these residues
util.cbay
; # color N blue, O red, H white and C yellow -> for more options press
tab after you typed in "util.cba" into the command line
color grey50, ele C ; # color carbon atoms grey
#util.chainbow("4eiy and not het") ; # the protein chain is colored
as rainbow
show sticks, ligand
color gold, ligand and ele C
set valence, 1, ligand ; # value 1 -> show valences (double
bonds ...) for the ligand; value 0 -> don't show double bonds
# metal ions and waters
# ---------------------
color grey, ele ZN
set sphere_scale, 0.3 ; # adjust radius of spheres, you may add a
selection: set sphere_scale, radius, selection
show sphere, ele ZN ; # show metal ions as spheres
color red, resn HOH
show nb_spheres, resn HOH ; # waters are generally
named "HOH"
# set nb_spheres_size, 0.25 ; # change the size of the nb_spheres
# distances, interactions
# -----------------------
set dash_gap, 0.4
set dash_radius, 0.05
set dash_length, 0.3
#dist hbonds, ligand or env, ligand or env, mode=2 ; # this
command shows all polar distances
# this will include "interactions" that do NOT satisfy donor angle
criteria or valid donor/acceptor pairs
# specify interactions by clicking on the atoms and copy/paste selection
strings
#dist hbond1, /4eiy/B/A/ZMA`2401/N15, /4eiy/B/A/ZMA`2401/N15
show dashes, hbonds ; # using an "*" character acts as a wildcard
-> dashes are shown for e.g. for DIST1, DIST2, ...
hide labels, hbonds
color black, hbonds
# electron density maps
# ---------------------
#fetch 4eiy, type=2fofc, pdb1ed ; # load 2fofc structure
factors for this pdb id
#isomesh mesh1, pdb1ed, 1.0, ligand, carve=2.0 ; # generate
mesh from structure factors
#set mesh_width, 0.3 ; # line width of the
mesh
#color grey50, mesh1 ; # color of the mesh
#show mesh, mesh1 ; #
show mesh as object mesh1
# labels (don't, add them in inkscape!)
# ------
set label_color, black
set label_outline_color, black
set label_bg_color, back ; # set the overall background
color to the semitransparent boxes behind the labels
set label_size, 16
set label_font_id, 7
set label_position=[0.0, 0.0, 2.0] ; # shift label in x,y,z
direction
#label name CA and resi 100+101,"%s-%s" % (resn,resi) ; # label
selection in the style "HIS-18"
#label name CA and resi 100, "H100"
# viewpoint
# ---------
orient ligand ; # orients the ligand around the principal axes
center ligand ; # centers on the ligand
zoom ligand ; # zooms on a selection
# after you adjusted a good view press "Get View" or type in the command
line "get_view" and paste the view matrix here!
# ***********PASTE VIEW MATRIX HERE ************
# for final raytracing:
# --------------------
# Press Display, Quality, Maximum Quality or uncomment the following line
# util.performance(0) ; # Set "high quality"
# adjust draw/ray size to sensible values and save the values here for
later changes
# ray 1800, 1200 ; # ray tracing
# alternatively use the draw command to render the image with the Pymol
OpenGL rendering engine
# draw 1800, 1200
# saving the image to a PNG file
# png 4eiy_protein.png ;# cd to a suitable directory before or
include path
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