1. Pymol tutorial Refresher and advanced topics Chem258
Michael R. Sawaya and Duilio Cascio
Oct 14, 2016

2. Goals
Illustrate an overview of the polymerase b complex with gapped DNA and ddCTP.
Make an improvement over this 1997 version 
downstream
oligo
ddCTP
template
primer
Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H. Crystal structures of
human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry Sep 16;36(37):

3. Access and Load coordinates
Download coordinates from PDB
In browser, type “
Don’t know the 4 digit PDB ID code for polymerase b? Type in search box: “polymerase beta human gapped ddctp”
click on link “1BPY”
click on “Download files”
select “PDB Format”
save 1bpy.pdb to your working directory
Open pymol window
Type “pymol”
Load coordinates in pymol
in pymol window, select “File menu” ”open”
browser window opens
navigate to directory where coordinates are located
select “1bpy.pdb”
molecule will appear in graphics window.
Next: How to script it.
polymerase beta human gapped ddctp

4. Write a pymol script load 1bpy.pdb, polbeta
Close your current pymol session.
Create a new file called “overview.pml”
gedit overview.pml &
Enter the following line in the script: load 1bpy.pdb, polbeta
Save this file. Don’t close gedit.
At the prompt, type: pymol overview.pml
Result: Polb molecule should appear in graphics window.
load 1bpy.pdb, polbeta
name of pdb file
short object name

5. Changing the view Rear clipping plane Front clipping plane rotate zoom
translate
drag
drag
Front clipping plane
Rear clipping plane
front
rear
drag
Shift
Shift
drag

6. Position the cursor on an atom and middle click
Bring an atom to the center
center
Position the cursor on an atom and middle click

7. Choose a representation
Default representation is “lines”.
Other representations:
cartoon
ribbon
spheres
surface
Click “S” for “show”.
Select “as”
“as” will replace current representation with the next selection
Select “cartoon”
Result: you should see the lines disappear and the cartoon takes it’s place. 1 2 3

8. Specify representation in your script
Close your current pymol session.
Continue editing the file called “overview.pml”
Add the following two lines in the script: hide everything
show cartoon
Save this file.
At the prompt, type: pymol overview.pml
Result: Polb molecule should appear in graphics window as a cartoon.
load 1bpy.pdb, polbeta
hide everything
show cartoon

9. Color by chains Default colors: all carbons green1
Default colors: all carbons green
Determine what chain IDs are present in 1bpy.
Select “C” button
select “by chain”
select lowest “by chain”
Result: each chain is colored separately. 2 3

10. Determine chain IDs T P A D left click on an atom of each color.
Note the chain IDs for
protein
template
primer
downstream oligo.
For example, you might see”
You clicked /polbeta/A/LYS’35/CA T P A D

11. Selection groups of atoms
“object”
Each object has an object name
We have only one object right now.
Our object is called “polbeta”
2) ”chain”
The chain ID. Usually it is a letter from A to Z.
We have chains A, D, P, and T.
3) “resid”
Residue number
Warning: Different chains can have the same residue number.
4) “resn”
Three-letter residue name. For example “lys” for all lysine residues.
5) “elem”
Element symbol from the Periodic Table
For example: “c” for carbon, “n” for nitrogen, “o” for oxygen…
6) “name”
The name of the atom.
For example: “ca” for alpha-carbon, etc.
general
specific
x y z
ATOM N LYS A N
ATOM CA LYS A C
ATOM C LYS A C
ATOM O LYS A O

12. Selecting ranges with“:” and “+”
A colon “:” between two quantities specifies the whole range between the quantities.
A plus “+” between two quantities specifies only the two quantities.
2) ”chain”
chain a:d selects all chains a, b, c, and d.
chain a+d selects all chains a and d
3) “resid”
resid 1:20  selects all residue numbers 1:20
resid 1+20  selects all residue nubmers 1 and 20.
4) “resn”
resn lys+arg+his  selects all lysine, arginine, and hisdine residues
5) “elem”
elem c+n+o  selects all carbon, nitrogen, and oxygen atoms
6) “name”
name c+ca+c+o+n  selects all backbone atoms
general
specific

13. Combining ranges with “and”, “or”
Colors only lysines between residues 1 and 100.
color red, resn lys and resid 1:100
Colors all lysines and all residues between 1 and 100.
color red, resn lys or resid 1:100
Colors all lysines not in the range 1 to 100.
color red, resn lys and not resid 1:100

14. Color subdomains; Create DNA object
Close your current pymol session.
Continue editing the file called “overview.pml”
Add the lines indicated in the right panel 
Save this file.
At the prompt, type: pymol overview.pml
Result: Polb will be colored by subdomain. DNA will be a separate object.
load 1bpy.pdb, polbeta
hide everything
show cartoon
color tv_yellow, resid 10:91 and chain A
color tv_blue, resid 92:148 and chain A
color tv_red, resid 149:261 and chain A
color tv_green, resid 262:335 and chain A
create dna, chain d+t+p
color gray20, dna
hide cartoon, polbeta and chain d+t+p

15. Subdomains are colored, DNA is a separate object

16. For printed figures Use a white background Turn off background opacity
bg_color white
It uses less ink.
It produces better contrast
Turn off background opacity
set ray_opaque_background, off
makes the background transparent
allows closer fit between panels.
Change color mode to “CMYK”
cmd.space('cmyk')
The default color space is ‘rgb” which is fine for display on computer terminals
printer colors are more limited
RGB
use for web media
CMYK
used for print media

17. For printed figures load 1bpy.pdb, polbeta hide everything
show cartoon
color tv_yellow, resid 10:91 and chain A
color tv_blue, resid 92:148 and chain A
color tv_red, resid 149:261 and chain A
color tv_green resid 262:335 and chain A
create dna, chain d+t+p
color gray20, dna
hide cartoon, polbeta and chain d+t+p
bg_color white
set ray_opaque_background, off
cmd.space('cmyk')
Add the lines indicated in the right panel 
Save this file.
At the prompt, type: pymol overview.pml
Result: Polb will appear on a white background.

18. CMYK colored

19. Show sticks for ddCTP, spheres for Mg2+
load 1bpy.pdb, polbeta
hide everything
show cartoon
color tv_yellow, resid 10:91 and chain A
color tv_blue, resid 92:148 and chain A
color tv_red, resid 149:261 and chain A
color tv_green resid 262:335 and chain A
create dna, chain d+t+p
color gray20, dna
hide cartoon, polbeta and chain d+t+p
bg_color white
set ray_opaque_background, off
cmd.space('cmyk')
show spheres, elem mg
show sticks, resn dct
Close your current pymol session.
Continue editing the file called “overview.pml”
Add the lines indicated in the right panel
Save this file.
At the prompt, type: pymol overview.pml
Result: Polb will be colored by subdomain. DNA will be a separate object.

20. sticks for ddCTP, spheres for Mg2+
see

21. Orient polb so DNA and chain path (N-to-C ) can be easily traced by eye.1
Adjust orientation.
Adjust front and rear clipping planes.
Press “Get View”
copy orientation matrix to pymol script.

22. Specify orientation matrix in script
bg_color white
set ray_opaque_background, off
cmd.space('cmyk')
show spheres, elem mg
show sticks, resn dct
### cut below here and paste into script ###
set_view (\
, , ,\
, , ,\
, , ,\
, , ,\
, , ,\
, , )
### cut above here and paste into script ###
Close your current pymol session.
Continue editing the file called “overview.pml”
Add the lines indicated in the right panel
Save this file.
At the prompt, type: pymol overview.pml
Result: Polb will be oriented as you chose.

23. Adjust the level of detail for the type of figure
category
Overview
Close-up
helices
Cylinders
Ribbons
Loop smoothing
Yes
No, use true path
Secondary structure
Widen for easy labeling
Normal to reduce emphasis
Bond radius
Thicken for visibility
Normal
Number of bonds
Minimize
As many as needed

24. Show bases in DNA (no sugars).1 2 3
Rings & Bases
Side Chain Helper
Round Helices
Cylindrical Helices
Flat Sheets
Fancy Sheets
Smooth Loops
Discrete Colors
Highlight color
Filled Rings (Round edges)
Filled Rings (Flat edges)
Filled Rings (with border)
Spheres
Base ladder
Bases & Sugars
Bases Only 4 5
Filled Rings (Flat edges)
Bases Only

25. Show bases in DNA (no sugars).
Filled Rings (Flat edges)
Bases Only

26. Show cylindrical helices1 2
Rings & Bases
Side Chain Helper
Round Helices
Cylindrical Helices
Flat Sheets
Fancy Sheets
Smooth Loops
Discrete Colors
Highlight color 3

27. Cylindrical helices

28. Widen beta-strands 1 2
change to 2.4 4 3

29. Wider beta-strands

30. Increase loop and helix radii1 2
change to 2.5 4
change to 0.5 5 3

31. Thicker loops and helices

32. Thicken bonds on ddCTP 1 2
change to 0.55 4 3

33. Thicker bonds on ddCTP

34. Quiz: How do you change the color of ddCTP and Mg to gray70?
color gray70, resn dct or elem mg

35. Settings to reduce details
, , ,\
, , ,\
, , ,\
, , ,\
, , ,\
, , )
### cut above here and paste into script ###
cmd.set('cartoon_ring_mode', 2)
cmd.set('cartoon_ring_finder', 2)
set cartoon_smooth_loops = on
set cartoon_cylindrical_helices = on
set cartoon_loop_radius=0.5
set cartoon_helix_radius=2.55
set cartoon_rect_length=2.4
color gray70, resn dct or elem mg
set stick_radius=0.55
Close your current pymol session.
Continue editing the file called “overview.pml”
Add the lines indicated in the right panel
Save this file.
At the prompt, type: pymol overview.pml
Result: Polb will be oriented as you chose.

36. Ray tracing 1 not ray traced ray traced surfaces appear smoother
shadows traced

37. Meeting the resolution requirements for journals
ray 900, 700 1
Most journals require 300 dpi resolution at the minimum.
Estimate how wide your figure will appear in print.
Multiply the number of inches by 300.
If 3 inches wide, then the figure must be at least 900 pixels wide.
When ray tracing, specify number of pixels width, and height
“ray 900, 700”
Save the image with the png command
“png overview01.png”

38. Default ray trace mode is ray_trace_mode = 0
Object appears realistic.

39. set ray_trace_mode = 1 ray 900,700
Outlined
Gives definition to molecular boundaries.

40. set ambient = 1.0 ray 900,700 Cartoony
Simplified by lack of shadows and color gradients.

41. set ambient = 0.2 setting renderingshadowsblack
Moody
But, here they hide the nucleotide.
We need to change the light direction.

42. Change light direction1 2 4
change to [ , , ] 3

43. set light=[5.0000, 0.2500, 0.2000] ray 900,700 Halloween
What deep dark secret is locked away in the nucleotide binding pocket?

44. set light=[-0.0500, 0.0000, -1.0000] ray 900,700 Lit up pocket
From this direction, strong light hits the ddCTP.

45. Examples of David Goodsell images
Shows all atoms to convey a truer representation of the molecule, but somehow simplified.
topoisomerase
DNA polymerase h

46. set ray_trace_mode = 3 Goodsell like hide cartoon, polbeta
show spheres, polbeta and not chain d+t+p
hide spheres, resn hoh ray 900,700
Goodsell like
Showing all atoms gives a truer representation of the molecule.

47. Looks like a photograph of a real object.
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue
set light_count,8
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
QuteMol
Looks like a photograph of a real object.

48. The best figures tell a story without having to read the caption.
Padilla JE, Colovos C, Yeates TO. Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc Natl Acad Sci U S A Feb 27;98(5):

49. Bad labeling technique can make a good image difficult to interpret
Place labels as close as possible to target.
Use smaller labels for features in rear
User larger labels for features in front
Match the color of the label to the target

50. Responsible labeling Place labels as close as possible to target.
Use smaller labels for features in rear
User larger labels for features in front
Match the color of the label to the target

51. Pymol help Google it Nice examples of different styles:
Pymol scripts:
An introduction to biomolecular graphics.