Pymol

tips and tricks Gates, Kent S. Univ of Missouri

Appendix 1: Pymol Commands

Downloading Pymol
To download Pymol, go to www.pymol.org or Google Pymol.
The program is called Pymol. Go to "products" tab. Then the "Pymol" link.
Then look for "educational subscriptions" link or go directly via
http://www.pymol.org/educational . Then look for the words "register for
educational-use-only pymol" and the associated "register here" link.
Fill out an agreement that specifies academic use, then you get a code that allows
FREE downloading of the program.

Downloading a pdb file

Go to www.rcsb.org or Google pdb. At the pdb website, type into the search
bar at the top your assigned coordinates of for example, 1C83.

On the left side of the page are several drop-down menus. The second from
the top is Download Files. Click on this and it will drop down some options. Click
on PDB text and save the file where you can easily find it.

Opening a pdb file

In Pymol, open a file by clicking File -> Open Locate and click on the pdb
file you downloaded from the web. You should see the structure in the viewer of
Pymol.

Using the mouse

To get the most out of Pymol, a three-button mouse is required. The scroll wheel
can be used as a button by clicking and holding. Try out the mouse commands as
detailed below on your newly loaded protein structure.

On a single button laptop (Mac), you can rotate the protein simply by holding
down the button and sliding your finger on the track-pad. You can center the
protein in the window using option-click and you can zoom using control-click.
You change the size of the slice that you are viewing with control-shift-click.

Pymol tips and tricks Gates, Kent S. Univ of Missouri

Std Commands:

reset (double click on image window, reset on menu, centers protein in window)
select all, then type: center (centers structure in window)
hide all
show cartoon
show side chain, resi 215
SettingCartoonSide Chain Helper
color gray90
color atom (gives color by atom identity)
show spheres, resi 301
color white, resi 301
color gold, resi 200-221
hide everything, resi 301
zoom: option, click, slide on trackpad
move x/y on page: control, click, slide on trackpad

Rendering and Saving: Click on the Ray button (in the top right corner of the
Pymol interface). It will take a few seconds to render. To save the snapshot (select:
File Save Image)

Rock: Click rock button in the upper right corner of the user interface.

Appendix 2. Pymol Tricks

Zoom resi X-X or zoom resi X (zooms to a section of the protein)

Orient (resets the view to normal)

Center the image: center

If the center of rotation seems "off" try these things: middle click on the desired
rotation center. You can also pull down the action menu of one of the ligands or
crossclusters and click "center". JJT.

Under the menu: Settings Cartoon Fancy Helices you can get cool looking
tubular edges to the helices. A nice touch.

Altering the properties of individual atoms in the structure: Control click a

menu appears on top of the atom. In this menu, under heading of atom you can
color, show, label, etc.

Measuring distances in the structure. Under the Wizard menu, select

measurement. Then click sequentially on the two atoms of interest. A yellow
ruler appears between them. This function stays on until you click done in the

Pymol tips and tricks Gates, Kent S. Univ of Missouri

measure window on the right side of the GUI. You can hide the distance label by
PyMOL>hide labels

Selecting a set of residues: select aas, resn cys

or select aas, resn cys + phe

or, in a DNA duplex select aas, resn a + g

To name a selection, for example: set_name sele, Alanines

Selecting all carbons: sele symbol c

(coloring carbons gray helps me because I cant see yellow sulfurs against the green
default color that Pymol uses for carbons)

Select all Gly: sele resn gly

Selecting a set of residues: sele resi 1-10

or: sele resi 1+5+7

Selecting all and carbons: sele name ca+cb

Selecting helices, sheets, loops: sele ss h OR sele ss s OR sele ss

One could also color helices, sheets, and loops, e.g.: color purple, ss h

Hide solvent: hide (solvent)

Change background color to white: bg_color white

Electrostatic potential surface: On the right menu of objects and selections (the
GUI), for example: under the A heading for 1C83_PTP1B_ligan, go to generate
then vacuum electrostatics then protein contact potential (local).

Add hydrogens to protein: h_add 1C83

You can make a surface view partially transparent (0-1) so that you can see the
cartoon beneath: show surface THEN type: set tranparency=0.5 (0.1 is less
transparent and 0.9 is more transparent).

Spheres can also be made transparent (0-1): set sphere_transparency=0.7

Size of spheres can also be changed (0-1): set sphere_scale=0.5 (Im not sure
what the default size is just have to play around with this)

The extent of depth-cued fog (0-1) is controlled by: set fog=0.5 (In my
experience this effect is only striking when the background is white. Again, Im not
sure what the default setting is zero is less foggy, one is more foggy).

Pymol tips and tricks Gates, Kent S. Univ of Missouri

The use of antialias reportedly greatly affects the quality of the image after ray-
tracing (and the also the time that rendering will require). Antialias is either on or
off. Set antialias=0 or 1 (before clicking ray).

Structural alignment of two homologous proteins:
In this example, you are going to align PH acylphosphatase (1w2i) and
bovine acylphosphatase (2ACY).
File -> Open -> 1w2i_nowat.pdb
File -> Open -> 2ACY.pdb

Pymol> align 1w2i_nowat, 2ACY
you should see the following in the text window:
ExecutiveAlign: 446 atoms aligned
ExecutiveRMS: 23 atoms rejected during cycle 1 (RMS=0.86)
ExecutiveRMS: 20 atoms rejected during cycle 2 (RMS=0.63)
Executive RMS = 0.541 (403 to 403 atoms)
In this case, the RMSD is 0.541
More often, people report Ca RMSD values which can be determined by:
Pymol>align 1w2i_nowat and name ca, 2ACY and name ca

How to handle structures that are dimeric, trimeric, etc.
Each subunit usually has a chain identifier a, b, c
Often it might be desirable to view just one subunit
Type:
- hide everything, all
- show cartoon, chain a
or
- show cartoon, chain a
- hide everything, not chain a
or
-hide everything, all
-show cartoon, chain a
show sticks, chain a and resi 213-216
if, during manipulation of the protein, things on the invisible subunits show up,
just type hide everything, not chain a again.

((Alternatively, it might be preferable to open the .pdb file using a program like
TextEdit on the Mac. Then, simply delete the coordinates for one or more of the
monomers)).

Or..

How about when there are two proteins shown in the unit cell, but I only
want to look at one (and get rid of the other)? under display menu select
sequence on. A bar will appear above the structure showing the amino acid sequence
of all protein chains in the window. Use option-shift to select all aa for one chain. Then
on the right for the (sele) go to the A (actions) menu and select remove atoms. Second
protein gone!

Pymol tips and tricks Gates, Kent S. Univ of Missouri

Pymol has no ball-and-stick mode; however, it can be simulated with a

combination of spheres and sticks.

>show spheres

>show sticks

>set sphere_scale, 0.3 (0.15, for small little knobs)

>set stick_radius, 0.2

sticks and balls will be the same color. If different colors are desired, this can
be achieved by creating separate objects for each.

How do I crank-up the glossiness of rendered atoms?

Type> set spec_power = 200 (# in range 20 250)
And> set spec_refl=1.5 (# in range 1.0 - 2.0)
Note that the shadow options in the Display menu of the external GUI may modify
these parameters.

Explore the Actions menu. For example: Locate the molecule name you loaded in
the right hand menu bar, On the same line as your molecule, click on A (Actions) ->
preset -> pretty

Showing entire structure when only half of the structure is shown due to
symmetry. (Often in DNA structures).
-click on A (actions) -> generate -> symmetry mates -> within 5 A.
Then go to the all heading and hide all then one-by-one show the
selections until you find the pair in which you are interested.

Generating symmetry pairs in a structure (longer explaination of the topic
above). Many DNA structures will show only one strand of the duplex because the
structure is symmetrical.

View the molecule in cartoon format. Pymol can use the symmetry information
(indicated in the text file you downloaded) to generate the symmetry related molecules.
- Click on A (actions) -> generate -> symmetry mates -> within 5

Zoom out a bit and you will see that Pymol generated quite a number of
neighboring molecules that are all present in the crystal and related by crystallographic
symmetry. I have colored the original molecule differently from the rest using the color
boxes on the right side of the molecule menu. You can make the same change to all

Pymol tips and tricks Gates, Kent S. Univ of Missouri

molecules by operating on the top all line. You can show the crystallographic unit cell
by selecting S -> cell (this is typically not helpful to me. Move on to the next step to find
the symmetry pair).

You must manually determine what the correct biological dimer pair by
undisplaying successive molecules by clicking on their names in the menu. Note that it is
not always obvious which molecule is the correct pair, even to people who have studied a
protein for years. You must use your best judgment.

-Undisplay them all by clicking on the all entry, then turn on the original
molecule and then go down the list one will look right.

Displaying the interaction diagram for a ligand. Go near the bottom of the
Summary page in the pdb (this typically the first page you land on). Find the
window entitled Ligand Chemical Component. Look for the Interactions
heading. Click on the window to see the interaction diagram. At the bottom of the
image click download to capture a .png file that you can save and open with
preview (on a Mac).

Should you ever want to show the phosphate trace of a nucleic acid
molecule:
def p_trace(selection="(all)"):

s = str(selection)

cmd.hide('lines',"("+s+")")

cmd.hide('spheres',"("+s+")")

cmd.hide('sticks',"("+s+")")

cmd.hide('ribbon',"("+s+")")

cmd.show('cartoon',"("+s+")")
cmd.set('cartoon_sampling',1,"("+s+")")
cmd.set('cartoon_tube_radius',0.5,"("+s+")")
cmd.extend('p_trace',p_trace)

Pymol tips and tricks Gates, Kent S. Univ of Missouri

Building In Pymol. Only useful for visualizing thought experiments does not
generate reliable, energy-minimized (realistic) protein structures.

(Need a three-button mouse for this, SWITCH MOUSE TO 3-Button EDITING MODE!)

Moving waters and ligands:

Moving waters and ligands is easy. Just remember to set mouse into
editing mode first!

For atomic waters, just CTRL-left-click and drag.

For multi-atom ligands, CTRL-middle click on an atom, and then SHIFT-
middle-click on that same atom to drag it around.

SHIFT-left-click on that same atom can be used to rotate the entire
fragment.

Moving entire loops:

In the menus, go to: Mouse -> 3 Button Edit

In the menus, go to: Build -> autosculpt

Sele resn 367-370 (use number range appropriate for your protein)

Control-shift-left-click DRAG and the whole loop moves while Pymol does its best
to keep the bond angles reasonable.

Changing the conformation of a single side chain. Rotating about a single bond:

In the menus, go to: Mouse -> 3 Button Edit

Control-right click on bond that you want to rotate. (or double-right-click)

Then control-left click DRAG the mouse after grabbing one of the substituents
on the end of the bond and the bond (and its substituents) will rotate.

Moving a single atom within a larger structure

In 3-button editing mode, double-click-and-hold on the atom then drag it where

you want it!

Drawing a new bond:

In 3-button editing mode, left-click on two atoms. Then under the Build menu
select create bond.

Pymol tips and tricks Gates, Kent S. Univ of Missouri

Deleting a bond:

In editing mode, select the bond using Ctrl-right-click, then either unbond pK1, pK2
or hit Ctrl-D

Deleting an atom

In 3-button editing mode: left-click on an atom then hit Crtl-D

Building a carbon chain

In 3-button editing mode, select a hydrogen atom by left-clicking on it, then hit:
Crtl-Cthis adds a CH3 group. Then, select a hydrogen atom on the end of the
growing chain and hit Crtl-C again, etc.

Manual Docking in PyMOL

1. Open the small molecule pdb file.

2. Go to the File menu and open the macromolecule pdb file. Now both players are
in the viewing window.

3. To selectively move the small molecule into position: Switch to 3-button edit
mode, and:

(a) shift-center click moves the molecule in x-y plane

(b) shift-right click moves it in and out on z-axis

(c) shift-left click rotates the small molecule.

(with no-shift the entire ensemble can be rotated etc.)

4. To save files as a pdb (instead of a PyMOL session, for example). Type: select all
in the command line. Hit enter. Then, in the A (action) menu for the sele you
just created, pick rename selection. A line appears in the viewer and you can type
in the name. Hit enter. Then, go to: File menu -> Save Molecule -> Find the one
that you just named on the list and Save it.

Altering the properties of individual atoms in the structure (color, etc). In 3-

button viewing mode, right-click a menu appears on top of the atom. In this menu,
under heading of atom you can color, show, label, etc. In 3-button editing mode,
command-right-click menu appears.