Quickie PyMol Tutorial - 30 min?

Stephen Curry
31 March 2006
What are we going to do this morning?

• Brief overview of the program

• Quick introduction to basic features
• Quick explanation of how to make nice figures using
scripts

• Just enough to get you started...

• You need to spend “hands on” time getting to know
the program
Introduction to PyMol
• What is PyMol for?
– looking at pdb files (protein, nucleic acid, ligands etc.)
– making publication quality figures (of models and maps)
– NOT for model building

• System requirements:
– computer (faster is better): PC (Windows/Linux), Mac (OS X)
– a 3-button scroll mouse
– works with hardware stereo

• Where can I get it?

– pymol.sourceforge.net
– current version: 0.99
– pymol.sourceforge.net/html/ - for the manual
Part 1 - loading, moving and displaying

• How do I...?
– Load a pdb file: (1) pdb loader; (2) open file
– Some display settings
– Create an object
– Use the mouse to move, zoom, slab, rotate (modifier keys)
– Use the object menus: A, S, H, L, C
Display options
Colour an object
– Navigate contextual menus
– Display the sequence
– Select residues
– Save my work
How do I start the program?
Double-click the
application icon (?)

or

From a terminal
window, type “pymol”

You should see a

command window and
a graphics window
(may be combined)

DEMO
How do I load a PDB file
• Download a pdb file directly into pymol
– Make sure you are connected to the internet
– Plugin > PDB Loader Service
– type in the PDB ID (e.g. 2bhg)
– object appears with this PDB ID

• Load a “local” pdb file

– File > Open...
– select pdb file
– object appears with same name as pdb file

DEMO
Useful display settings...

Display > Background > white ----set background colour

Display > orthoscopic view ----no perspective distortion

Creating new objects
• To create an object containing just chain A of
2bhg (= FMDV 3Cpro)
– type in command (or graphics) window:
create 3C-a, (2bhg and c;a)

chain A
new
object brackets
required Boolean
name
operator
comma
required

DEMO
Using the mouse in the graphics window

• Unmodified controls
– Left - rotate molecule (x, y and, at edges, z)
– Middle - translate molecule (x, y)
– Right - zoom (=MovZ)
– Wheel - slab/clip
Menu at bottom right
• With shift key
– Right - up/down: clip front
- left/right: clip back

DEMO
Object menus: A, S, H, L, C
A is for Action

Navigation tools

Quick-draw tools

Assigning secondary structure

Object manipulation

NB: some of these

will have sub-menus

DEMO
S is for Show

Useful representations
H is for Hide

Same content as Show menu

Use Show and Hide to toggle

things on and off

L is for Label

Haven’t used this

DEMO
C is for Color

Lots of options

Mostly self-explanatory

Color menu gives names

of ready-made colours that
can be used in scripts

DEMO
Contextual menus
• Left double click or right single
click to activate
– click on object or part of object
you want to manipulate
– more or less the same menus as
ASHLC

DEMO
Display the sequence

From menu:
Display > Sequence
or
click on “S” in mouse menu

Use the sequence to select

residues for modification
Access menus from the
sequence

DEMO
The settings menu

Settings > Edit all...

Lots of options!
Some explained here
Otherwise, make
educated guesses
and see what
happens
Saving your work

File > Save Session...

Enter filename as “my_file.pse”
Will save all your current settings (display objects, maps)

When you return to PyMol, load this file:

File > Open
Part 2 - making figures with scripts

• How do I make nice figures for publication?

– Using scripts
– Load molecules
– Assign/edit SS
– Define colours
– Molecule representation
– Showing sidechains - (problems with β-sheets)
– Colouring atoms by type
– Adding surfaces (as separate objects)
– Drawing maps
– Set view (get view); depth cueing
– Ray tracing
Fig. 1 - protein, ligands, sidechains, bonds

Secondary structure
CPK
Sticks
Surfaces
H-bonds
Domain colouring
Selection of residues
and atoms
Fig. 1 script - pt1
# Script name: hms1-pbz.pml (hsa-myristate-site1-phenylbutazone)
#
# Close-up of drug site 1 in hsa-myr-pbz
#
#define initial, view, cartoon parameters
@pymol_setup.mac Set global parameters (see next)

load ../pdb/hsa-myr-pbz.IIA.pdb, hsa Load pdb file; don’t

hide
display anything
#define secondary structure
Use pymol to do it: dss
#dss hsa
@hm_ss or
rebuild use dssp and append ss definitions to
hide pdb file
or
#define hsa colour-scheme
set_color hsa_red, [1.0, 0.1, 0.5] Do it yourself: @hm_ss (see next slide)
set_color hsa_light_red, [1.0, 0.7, 0.7]
set_color hsa_green, [0.0, 0.65, 0.0]
set_color hsa_light_green, [0.6, 1.0, 0.6]
Define some useful colours (and
set_color hsa_blue, [0.0, 0.5, 1.0] names) - for a consistent look
set_color hsa_light_blue, [0.5, 1.0, 1.0]
RGB triple
Global settings
Script/macro used to set some global parameters

# pymol_setup.mac
#
#initial setup
viewport 600, 600 ---size of graphics window
set auto_zoom, off ---don’t zoom in on new objects
set auto_show_lines, off ---don’t automatically display loaded pdb files
set auto_show_selections, off ---don’t automatically display selections

#cartoon parameters
set cartoon_fancy_helices,1 ---nicer helices (personal choice)
set cartoon_discrete_colors,1 ---can’t remember
set cartoon_highlight_color, grey60 ---inside of helices light gray
set cartoon_dumbbell_length,1.0 ---defines width of helix ribbon!
set cartoon_rect_length,1.40000 ---defines width of β-strands
set cartoon_loop_radius,0.3 ---width of tube used for loops
set cartoon_smooth_loops=0 ---no smoothing (if sidechains needed)
Global settings
pymol_setup.mac continued...

# set radius of dashed lines (i.e. Hbonds)

set dash_radius, 0.1

#view & ray-tracing parameters

set orthoscopic=1 ---no perspective distortion
set ray_shadows=0 ---no shadows
set depth_cue=1 ---depth cueing on (realtime display)
set ray_trace_fog=1 ---ray-trace depth cueing
bg_col white ---white background colour (fashionable)
#set surface_quality=1.0 ---smooth surfaces (off by default - slows things down)
set antialias=1.0 ---smoother lines when ray-tracing
set two_sided_lighting, on ---lighting effect

#memory allocation for faster ray tracing

set hash_max, 400 ---play around with this value to see if it helps!
hm_ss: set the secondary structure
#define secondary structure for HSA-FA
complexes

#set everything to loop

alter 3-584/, ss='L'
...
#now define helices in HSA alter 283-291/, ss='H'
alter 6-14/, ss='H' alter 305-310/, ss='H'
alter 16-29/, ss='H' alter 315-321/, ss='H'
alter 36-55/, ss='H' alter 323-336/, ss='H'
alter 66-74/, ss='H'
alter 343-358/, ss='H'
alter 80-83/, ss='H'
alter 85-92/, ss='H' alter 366-368/, ss='H'
alter 95-102/, ss='H' alter 373-397/, ss='H'
alter 120-129/, ss='H' alter 400-414/, ss='H'
alter 132-145/, ss='H' alter 420-436/, ss='H' For β-strands:
alter 151-168/, ss='H' alter 442-466/, ss='H' alter 100-110/, ss=’S'
alter 174-205/, ss='H' alter 471-478/, ss='H'
alter 208-222/, ss='H' alter 486-490/, ss='H'
alter 228-246/, ss='H' alter 504-507/, ss='H'
alter 250-266/, ss='H'
alter 513-515/, ss='H'
alter 268-270/, ss='H'
alter 276-280/, ss='H' alter 518-535/, ss='H'
... alter 541-559/, ss='H'
alter 566-584/, ss='H'
Fig. 1 script - pt2
#colour dfhsa molecule (typically residues 5-582)
Colour the HSA
color hsa_red, (i;5-106)
color hsa_light_red, (i;107-196) molecule by domain
color hsa_green, (i;197-296) (see next for more
color hsa_light_green, (i;297-383) selection syntax)
color hsa_blue, (i;384-496)
color hsa_light_blue, (i;497-582)

#create dom2 and dom3 based on single structure loaded above Create an object
@hm.dom23.mac containing domains
#define drug colour scheme 2 and 3
@drug_colours.mac

#draw drugs as sticks and colour by atom type Create an object called “drugs”
create drugs, (hsa and (i;2001 or i;1009)) that displays two ligand
show sticks, drugs
@drugs-stick-rad.mac
molecules as sticks
color pbz_col, (i;2001 and e;C)
color fa_col, (i;1009 and e;C) Colour by atom type
color blue, (drugs and e;N)
color red, (drugs and e;O)
color green, (drugs and n;CL)
Selection syntax - some examples

i;99-105 residues 99-105 inclusive (i = index?)

i;99:105 residues 99-105 inclusive
r;tyr all Tyr residues (r = residue name)
c;a chain A (c = chain)
n;N atoms named “N” (= main-chain nitrogen)
n;CA atoms named “CA” (=alpha carbon)
(get to know the atom names in pdb files)

e;C all carbon atoms (e = element)

More macros defined
#hm.dom23.mac
#generate domains 2 and 3 to show drug site 1 in a single structure
#
create dom2, (i;194:297 or i;148:151)
show cartoon, dom2 Boolean
create dom3, (i;340:350 or i;479:483 or i;445:459) algebra
show cartoon, dom3

#drug_colours.mac #drug_stick_rad.mac
# site 1 (primary) set stick_radius, 0.22, drugs
set_color aza_col, [1.0, 1.0, 0.75]
set_color cpf_col, [0.75, 0.75, 0.25]
set_color dzp_col, [1.0, 0.75, 1.0]
set_color hal_col, [0.25, 0.25, 0.25]
set_color imn_col, [1.0, 1.0, 0.5]
set_color iod_col, [1.0, 0.5, 0.5]
set_color oxy_col, [0.25, 0.75, 0.5]
set_color pbz_col, [0.0, 0.75, 1.0]
etc...
Fig. 1 script - pt3
Create an object called “surf”
create surf, (hsa and i;2001)
show surface, surf which shows the surface of
colour lilac, surf residue 2001 (=pbz).
set transparency, 0.6, surf Make semi-transparent.
create surf1, (hsa and i;1009)
show surface, surf1 Create an object called “surf1”
set_color light_yellow, [1.0, 1.0, 0.2] which shows the surface of
colour light_yellow, surf1 residue 1009 (=FA).
set transparency, 0.5, surf1 Colour it differently
# add FA2 Make semi-transparent.
create fa-c, (i;1002 and e;C)
set sphere_scale, 1, fa-c Draw a FA molecule as a CPK
show spheres, fa-c
model by creating 2 objects
create fa-o, (i;1002 and e;O) (“fa-c” and “fa-o”).
set sphere_scale, 0.78, fa-o
show spheres, fa-o Make O atoms smaller than C
atoms (VdW)
color grey70, ((fa-c or fa-o) and e;C)
color red, ((fa-c or fa-o) and e;O)) Colour by atom type.
Fig. 1 script - pt4
# add sidechains for site 1 (sc1.mac) Create an object called “sc”
@sc1.mac
which shows selected
show sticks, sc
@sc-stick-rad.mac sidechains as sticks.
color grey70, (sc and (e;C and not n;CA)) Colour by atom type - but do
color blue, (sc and e;N) not re-colour the CA atom
color red, (sc and e;O)
color yellow, (sc and e;S)

# add sidechains for rest of pocket - based on pbz

create sc2, (hsa and (i;198 or i;206 or i;347 or i;481 or i;450:451 or i;454:455)
and not (n;O or n;C or n;N))
show sticks, sc2
@sc-stick-rad.mac
color grey70, (sc2 and (e;C and not n;CA))
color blue, (sc2 and e;N)
color red, (sc2 and e;O) Same again for another set of
color yellow, (sc2 and e;S) sidechains
More macros defined

#sc1.mac
#drug site 1 sidechains
create sc, ((i;150 or i;195 or i;199 or i;202 or i;211 or i;214:215 or i;218:219 or
i;222:223 or i;234 or i;238 or i;242 or i;257 or i;264 or i;291)
and not (n;O or n;C or n;N))
All one line!

Select specific residues and

exclude the following
mainchain atoms: N, O, C

More complicated Boolean

algebra...
Fig. 1 script - pt5
# add 343-344 to show h-bonds to Glu450
create 343, (hsa and ((i;343 and not (n;O)) or (i;344 and n;N))) Tricky bit to show
show sticks, 343 sidechain and some
@sc-stick-rad.mac
color grey70, (343 and (e;C and not n;CA))
mainchain atoms
color blue, (343 and e;N)
color red, (343 and e;O)

# add hydrogen bonds

distance dst1 = (/sc//A/ARG`218/NH2), (/drugs//A/pbz`2001/O2), 5.0 Define and draw H-
distance dst2 = (/sc//A/ARG`218/NE), (/drugs//A/pbz`2001/O2), 5.0 bonds
distance dst3 = (/sc//A/HIS`242/NE2), (/drugs//A/pbz`2001/O1), 5.0 Atom definitions are
distance dst4 = (/sc2//A/GLU`450/OE1), (/343//A/VAL`343/N), 5.0
distance dst5 = (/sc2//A/GLU`450/OE2), (/343//A/VAL`344/N), 5.0 horrible but you can
distance dst6 = (/sc2//A/ASP`451/OD1), (/sc//A/LYS`195/NZ), 5.0 get them by:
distance dst7 = (/sc//A/ARG`257/NH1), (/drugs//A/pbz`2001/O1), 5.0 Ctrl-shift-left click.
color yellow, dst1 Colour bonds yellow.
set dash_gap=0.4
hide labels

#set view
@s1-hm-cuview.mac
Define the viewpoint (see next)

#ray 1200,1200
Ray-trace and write out file (remove ‘#’ when ready)
#png hms1-pbz.png
Setting the viewpoint
You don’t have to type
# s1-hm-cuview.mac
this!
# close-up view of site 1 in hsa-myr
#
set_view (\ • Set the view you want
0.847002089, 0.519193769, -0.113906674,\ in the graphics window
-0.408921719, 0.773371875, 0.484395087,\ • Click on the “Get View”
0.339599967, -0.363719672, 0.867373824,\ button
-0.001291693, 0.898808300, -70.790878296,\
31.465492249, 12.112967491, 12.206689835,\ • Cut and paste the
52.887966156, 87.986236572, 1.000000000 ) set_view matrix into
your script (or macro)
Fig. 2 - protein with electron density

Loading maps
Display as mesh and/or surface
Controlling extent of map displayed
Fig. 2 script - pt1
# script: 3C_loopmap.pml
#
#setup global parameters Setup and load pdb file
@pymol_setup.mac

load wat4a_060310.2.A.pdb, 3C

set_color light_magenta, [1.0, 0.6, 1.0]

set_color light_orange, [1.0, 0.6, 0.3]
set_color light_green, [0.6, 1.0, 0.6] Define colours
set_color light_blue, [0.5, 0.75, 1.0]
set_color purple, [0.5, 0.25, 0.75]

cartoon loop, 3C Define cartoon representation

set cartoon_loop_radius,0.3, 3C
to be used (loop).
colour light_green, 3C
Create object called “prot”
create prot, (3C and (i;7-135 or i;150-208)) consisting of all residues except
show cartoon, prot
136-149). Draw cartoon
representation (loop)
Fig. 2 script - pt2
create prot-loop, (i;135:150)
hide everything, pro-loop
Draw and object called “prot-
show sticks, pro-loop
loop” showing residues 135-
colour light_orange, (pro-loop and e;C)
colour yellow, (pro-loop and e;S) 150 as sticks.
colour red, (pro-loop and e;O) Colour by atom type
colour blue, (pro-loop and e;N)

load k51e_sa1_fofc.xplor, difmap Load map (CNS format but

isomesh msh1, difmap, 2.0, pro-loop, 1.0, 0, 2.5 with .xplor extension!) and call
colour tv_blue, msh1 it “difmap”.
set mesh_width, 0.6, msh1 From “difmap, draw map as
mesh (creating object “msh1”).
Contour level=2, around object
“prot-loop (plus 1.0 Å buffer),
mesh_width = width of lines state=0 (?), carve=2.5
in the mesh Value of carve parameter is
most important for controlling
extent of map displayed
Fig. 2 script - pt3
isosurface sf1, difmap, 2.0, loop, 1.0, 0, 2.5 From “difmap, draw map as
colour grey90, sf1 a smooth surface (creating
set transparency, 0.5, sf1 object “sf1”). Use same
parameters as for msh1
set_view (\
0.522022903, -0.471787959, -0.710549474,\
-0.766768932, 0.105253145, -0.633219361,\
0.373555541, 0.875387847, -0.306816727,\
-0.000078557, -0.000008190, -75.465362549,\ Set view and ray
-15.310430527, -12.940036774, -9.453201294,\ trace as before
64.074295044, 86.465293884, 1.000000000 )

#ray 1000,1000
#png k51e_loopmap.cu.png

Comment out (to prevent ray

tracing) while you are refining
your script. Restore when you
want to generate an image file.
Summary/Key points

• Scripts can get very complex but once you’ve

done one, you can copy, cut and paste
• For a talk/paper you might make up to 30-40
images
• Use scripts/macros to get a consistent look
and to facilitate changing parameters across
many images
• You need to be organised...
Advanced topics (for next time...?)

• Not included but very useful:

– Setting the image filename within a script
– Making movies
– Aligning 2 molecules
– Displaying symmetry-related objects
– Calculating and displaying electrostatic surfaces

• For next time:

– Define what is meant by “ray-tracing” or “rendering”
– Show use of PyMol alongside nedit