Introduction to Pymol

http://www.pymol.orghttp://pymolwiki.org

• how do I load DPB file?– Plugin -> PDB Loader Service (2bhg)– File -> Open (locally stored)– command: load

• fetch 2bhg, load 2bhg• command is a keyword, followed optionally

by one or more comma-separated arguments

• color red, hetatm• color red• help show

Using the mouse

• Unmodified controls– Left - rotate molecule (x, y and, at edges, z)– Middle - translate molecule (x, y)– Right - zoom (=MovZ)– Wheel - slab/clip

Object menus (ASHLC)

Action

Navigation

Quick draw

Manipulation

Show

Hide

• same content as Show

• Use Show and Hide to toggle things on and off

Label

Color

• Rule: Once a selection is shown (S) it must be selectively hidden (H) as it is not removed when another selection (S) is made. Selections are therefore additive, which allows for the creation of images with mixed graphical representations.

• S -> Cartoon, H -> Lines• S -> as – you do not have to click S,H• Most options can be set within the

“Setting” menu within the top menu bar.• Settings -> Cartoon

• Changing the background to white:– Display -> Background -> White

• The “Display” menu within the top menu bar contains options for most options pertinent to displaying the image witin the PyMol viewer.

• “fog” within the back of the molecule – Display -> Depth Cue

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

Ligand rescue squad

• load 1BIW into Pymol• show as cartoon• recolor by secondary element• ligand is there, but it has disappeared!• rescue ligand:

– S > organic > spheres

Mouse selection

• Click on one of the spheres of the carotenoid ligand– pink dots (click anywhere to unselect)– a new name called (sele)– The name of the atom that was clicked appears within

the top text window of the “external GUI.”You clicked /2BIW.pdb2//B/TYR`322/OHSelector: selection "sele" defined with 12 atoms.

• This could be read as “you clicked atom OH which is on the 322nd atom in the file, and belongs to Tyrosine of chain B in the object created when opening file 2BIW.pdb2. The complete selection contains 12 atoms

• (sele) -> C -> by element -> CHNOS

Making images

• File -> Save Image As -> PNG• Raytracing (Ray button, top right), then

Save Image• even better quality, use command

– ray x, y (e.g. ray 2000, 2000 - dimension)

Action presets

• A -> Preset -> Default is similar to hide everything, show lines

• preset options will set some variables that are specific to these views and may change further drawings. To remove the effect of these presets affecting an object representation, use the A -> preset -> default.

• Let’s explore other presets.

• simple• b factor putty

– The segments with the highest temperature factor are shown as thicker cylinders. Regions of better resolution have thinner diameter and are usually found at the core of the protein. Mostly loops in the outside of the protein wobble: the core portions of the proteins usually appear more stable than the external loops. This is mostly useful for crystallographers but is a cool representation.

• technical– Color domains in separate rainbow colors and shows

backbone and side chains.• pretty and publication

• ligands– zoom in on the ligand site and show the protein as

backbone except in the near vicinity of the ligand where side chains are shown. The ligand is depicted as a thicker cylinder

– to zoom out, simply click on the A > Zoom• ligand sites

– pertinent to looking closely at the ligand in it’s binding pocket

– solid surface, 2biw > C > Yellows > Sand, select ligand stick, sele > C > Blues > slate

– Note: If you are preparing a figure for a black and white print publication, it might be advantageous to use the various gray scales, black, and white within the “grays” option.

– explore others by yourself

Measuring distances

• from menu: Wizard -> Masurement• click on the first atom in ligand, click on the

second atom in ligand• change the color to white (ASHLC)• When you are done using the “Measurement”

panel on the bottom right click Done.• If you no longer need to display the distance

object, click Delete All Measurements. Alternatively you can use the corresponding “A” menu and select the delete option.

Clipping• Clipping planes are imaginary

planes in the front and back of the molecule. Parts of the molecule that are outside the planes are “clipped” and therefore invisible. This is very useful for complex or large structures.

• To move clipping planes press shift and the right mouse button simultaneously while dragging up and down. As an exercise, try to remove some of the molecular surface

Save your work

• File -> Save session– *.pse, binary file– save your objects, settings

• File -> Open

Pymol command language

• most interaction with PyMOL is via a scripting language, not all functions are available from menus

• keyword followed optionally by one or more comma-separated arguments, e.g. color red, hetatm – colors all non-protein atoms red, color red – all atoms are red

• in most cases 1st argument is specific to command used, while the 2nd argument is the name of the object/selection

commonly used commands

more in PyMol docs (paid, obsolete at http://pymol.sourceforge.net/html ) or at wiki http://www.pymolwiki.org/index.php/Category:Commands

PyMOL Reference card: http://pymolwiki.org/images/7/77/PymolRef.pdf

• download 1GBV in PDB format• load it into Pymol as 1gbv object

help showload 1gbv.pdb, 1gbvhideshow cartoonhide cartoon, chain Ashow ribbon, chain Aset ribbon_width, 5hide cartoon, chain Bshow spheres, chain Bhide cartoon, chain Cshow sticks, chain Ccolor red, chain Acolor blue, chain Bcolor orange, chain C

Save your work• PyMOL script – text file with commands, each at

one line (see example.pml at the website)• *.pml• comments begin with # end_of_line• run script from PyMOL: @example.pml• or from command line as

pymol example.pml • save the image

– ray– png

Selections

• chain A is an example of a selection• two selection syntaxes: hierarchical and

algebraic• hierarchical

/model/segment/chain/residue/atom– if patterns start with slash, the selection is

worked out left-to-right, if the first slash is missing, the patterns are worked out right-to-left

– select ///A/10 #residue 10 in chain Acolor red, selecolor atomic

– select ////10-20/CA # atoms CA in residues 10-20 # (any chain)

– select 42/C+N (C,N?) #atoms C and N in residue 42show spheres, sele

• algebraic–combine terms (e.g. chain A) using

logical operators (AND, OR, NOT) – select wc, chain A # wc is the name of selection– select chain A and resi 10:20 # residue number– select resn ALA and name N # backbone nitrogens # from ala

residues– select elem O and not name OH # oxygen atoms

# except hydroxyls

• The items in a list of identifiers are separated by plus signs (+) only. Do not add spaces within a list of identifiers. The selector resi takes (+)-separated lists of identifiers: – select nt, resi 1+2+3– select nt, resi 1-3– don’t combine these two (1-3+6 is wrong)

property

example

symbol e. chemical symbol, select polar, symbol (e.) o+n

name n. atom names, select carbons, n. ca+cb+cg+cd

resn r. residue names, select aas, r. asp+glu+asn+gln

resi i.

residue numbers, select mults10, i. 1+10+100+1000

select one, resi 10zoom one

chain c. chain ID

ss - secondary structure type, select allstrs, ss h+s+l+""

Selection algebra• and, or, not etc.• how would you select resid 27 and resid

28?

property short example

not s1 ! s1 atoms that are not included in s1

and & atoms included both in s1 and s2

or | atoms included in either s1 or s2

in - s1 atoms whose name, resi, resn, chain match s2 atoms

like l. s1 atoms whose name, resi match s2 atoms

property short examples1 around X s1 a. X atoms with centers within X Angstroms of the

center of any atom in s1 select near10, resi 10 around 5

s1 expand X s1 e. X Expands s1 by all atoms within X Angstroms of the center of any atom in s1 select near10x, near10 expand 3

s1 within X of s2

s1 w. X of s2

Selects atoms in s1 that are within X Angstroms of the s2

byres s1 br. s1 Expands selection to complete residues select cmplt, byres near10

neighbor s1 nbr. s1 atoms directly bonded to s1select vic, nbr. resi 10

s1 extend X s1 ? X Extends s1 by X bonds connected to atom in s1select connect_x, near10 extend 3

# selects atoms that are part of chain a, but not # residue number 125. select chain a and (not resi 125)  

# The following two selections are equivalentselect (name cb or name cg1 or name cg2) and chain A  

select name cb+cg1+cg2 and chain A

• select residue 10 in chain B (name it cpk10)

• show it as cpk, zoom at it• hide cpk10 selection

• make a selection called bb containing C, O and N atoms

• count atoms in selection (count_atoms)• remove residue no. 5 (remove)• count atoms again

objects vs. named-selections• PyMOL creates an object-name to locate data when you

load a data file.• Making selections is a way of pointing to a subset of that

data.• Selections are in parentheses in control panel.• When you delete a selection-name, the data are still

found under the object-name, but the data are no longer organized as the selection. In contrast, after you delete an object, you must reload the data to have access to it again.delete

• PyMOL can hold several objects at the same time (load 1gbv and 1bna) disable, enable

TIP: get rid of pink dotsselect bb, name c+o+n+ca, disable bb, color red, bb

• Named selections are static. Only atoms that exist at the time the selection is defined are included in the selection, even if atoms which are loaded subsequently fall within the selection criterion

• clear your workplace, load 1gbv• make selection called static containing all

1gbv atoms• count atoms in static• add hydrogens (h_add)• count atoms in static, compare with count atoms

in the whole structure

Single word selectors

Selector Short form

Description

all * All atoms currently loaded into PyMOL

none - No atoms (empty selection)

hydro h. All hydrogen atoms currently loaded into PyMOL

hetatm het All atoms loaded from Protein Data Bank HETATM records

visible v. All atoms in enabled objects with at least one visible representation

polymer All atoms on the polymer (not het).

Point of view

• zoom• orient

– aligns the object or selection so its largest dimension is shown horizontally, and its second largest dimension is shown vertically

• view– store orientations and recall them later –view v1, store; view v1, recall; view v1