1. Introduction to Pymol
Nov. 2010

2. Lab Agenda Brief overview of PyMol
Quick introduction to basic features
Demonstration of how to generate figures for publication
Just enough to get you started
You need to spend “hands on” time getting to know the program

3. Introduction to PyMol What is PyMol for? Where to get it?
Visualizing pdb files
Generating publication quality figures
Not for model building (Coot, Phenix)
Where to get it?
User name: dec2010
Password: mol2View
Expire on Jan 1st, 2011

4. How do I start the program?
Double-click the application icon
command window
graphics window
DEMO—start program

5. How do I load a PDB file Download a pdb file directly into pymol
Use command line
Type “fetch 1A4U”
Load a “local” pdb file
File -> Open…
select pdb file
object appears with the same name as pdb file
1A4U
DEMO—load 1A4U

6. Useful display settings
Display -> Background -> white OR
“bg_color white” set background color
Display -> orthoscopic view
“set orthoscopic=1” no perspective distortion

7. Using the mouse in the graphic window
Default mouse controls
Left: rotation mode
Middle: translation mode
Right: zoom in/out (=MovZ)
Wheel: slab/clip
Other combinations
Menu at bottom right
DEMO

8. Creating new objects
To create an object containing just chain A of 1A4U (apo form of Drosophila ADH)
type in command widow:
create 1a4u-a, (1A4U and chain A)
new object name
Boolean operator
brackets required
Comma required
DEMO—create object

9. Object menus: A, S, H, L, C

10. DEMO—orient, preset, rename
A is for Action
Navigation tools
Assigning secondary structure
Object manipulation
DEMO—orient, preset, rename

11. S is for Show H is for Hide Different types of representations
Basically the same
content as show menu
Use Show and Hide to toggle things on and off
DEMO

12. L is for Label Not very useful
Usually label in PowerPoint or other imagine process software
DEMO

13. DEMO—element, chain, ss, spectrum
C is for Color
Lots of options
Most self-explanatory
Color menu gives names
of ready-made colors that
can be used in scripts
DEMO—element, chain, ss, spectrum

14. 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

15. Display the sequence From menu: Display -> Sequence or
click on “S” in mouse
menu
Use the sequence to select residues for manipulation

16. The settings menu Settings -> Edit all… Lots of options!
Make educated guesses and see what happens

17. Saving your work File -> Save Session… File -> Open
Enter filename as “figure1.pse”
Will save all your current settings (display objects, maps)
When you want to continue on previous work, load this file:
File -> Open

18. List of PDB files Apo form: 1A4U Binary complex (NAD): 1B14
Ternary complex (NAD-acetone): 1B15
Ternary complex (NAD-3-pentanone): 1B16
Ternary complex (NAD-cyclohexanone): 1B2L
Benach, J., Atrian, S., Gonzalez-Duarte, R. and Ladenstein, R. (1999) The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: observation of an enzyme-bound NAD-ketone adduct at 1.4 A resolution by X-ray crystallography. J Mol Biol, 289,

19. Figure 1
Superposition of two subunits from 1A4U (no substrate, apo form) and ternary complex 1B16 (NAD-3-penanone)

20. Re-illustration of Figure 1
@open pymol, input the following command lines bg_color white set orthoscopic=1 fetch 1A4U create 1a4u-a, (1A4U and chain A) fetch 1B16 create 1b16-a, (1B16 and chain A) align 1a4u-a and name CA, 1b16-a and name to cartoon representation, show NAD-3-pentanone as sticks #options for ray-tracing set ray_shadow=0 ----no shadows when ray-tracing set ray_trace_fog=1 ----ray-trace depth cueing on set surface_quality= smooth surfaces (off by default-slow!) set antialias= smoother lines when ray-tracing
DEMO

21. RMSD (Root Mean Square Deviation)
The Root Mean Square Deviation is a numerical measure of the difference between two structure. It is defined as:
where is the number of atoms whose positions are being compared, is the position of atom in structure a, and is the position of atom in structure b.
RMSD is a numerical measure to quantify how different two structures are.

22. Figure 2
Arrangement of amino acid side-chains at the active site entrance (Thr186 to Phe 192)
1B16
“induce-fit”
1B2L
This region is often partly disordered or has higher B-factors than the rest of the structure and change its conformation to accommodate the sbustrate

23. Fig. 2A
@open pymol bg_color white set orthoscopic=1 fetch 1b16 create label_residue, (1b16 and chain A and resid , 95, label_residue as stick, adjust the view as shown in 1b16 as cartoon, also show as stick, hide label_residue set stick_ball, 1 set stick_ball_ratio, 1.5 set cartoon_side_chain_helper, 1 #options for ray-tracing set ray_shadow=0 ----no shadows when ray-tracing set ray_trace_fog=1 ----ray-trace depth cueing on set surface_quality= smooth surfaces (off by default-slow!) set antialias= smoother lines when ray-tracing

24. Re-illustration of Fig.2A
Thr191
Phe192
Leu95
Tyr151
Val189
His190
Leu188
Pro187
Thr186

25. Cys 217 at the active site DEMO Cys217
create NAD, (1b14-a and resn NAD)
create near5_NAD, (1b14-a byres NAD around 5)
create near_NAD_cys, (near5_NAD and resn cys)

26. Practice 1
Re-illustrate figure 2b
ternary complex (PDB ID: 1B2L)

27. Practice 2
Re-illustrate Figure 9.