PyMOL	
	
	
Open	the	pdb-file	
	
• PyMOL	->	File	->	Open	(*.pdb/*.cif/*.pse)	
	
• fetch		pdbID					(for	example:		fetch	1k1g)	
	
Interface	
	
	
	
A	=>	actions	
S	=>	show	(representation)	
H	=>	hide		(representation)	
L	=>	label		
C	=>	coloring		
	
Mouse	mode	=>	3-Button	Viewing/Editing	
	(PyMOL	->	Mouse		….	options	for	mouse	modes)		
	
State	=>	assembly					1/20	(NMR	structures)	
																																				1/1	(crystall	structures)	
F	=>	full	screen	mode	
	
S		=>	show	sequence		(PyMOL	->	Display	->	SequenceMode)	
	
	
	
NMR	vs	crystal	structure	
	
NMR	
->	hydrogen	atom	 	
• set	all_states,	on		
• intra_fit		name		
• split_states																																																																			
	
Crystal	structure	
->	no	hydrogen	atoms														PyMOL	->	Actions	->	add	hydrogens								
• hide	(solvent)							
• remove	what	
	
	
Representation	
	
• split_chains	
	
Rename	chain/selection	
	
• set_name	old	name,	new	name												(set_name	1k1g_A,protein)								
																																																																					(set_name	1k1g_B,	RNA)	
	
Hide		
	
PyMOL	->	Hide	(H)	->	lines/sticks/cartoon/ribbon/labels/…	
	
• 	hide	what					(hide	lines)	
	
Show	
	
PyMOL	->	Show	(S)	->	lines/sticks/cartoon/ribbon/labels/…	
	
• show	what				(show	cartoon)	
	
• dss		(defines	secondary	structure	based	on	backbone	geometry	and	hydrogen			
																						bonding	patterns)				
																											
Color	
	
PyMOL	->	Color	(C)	->	by	element/chain/side	chain/representation/	
	
Label	
	
PyMOL	->	Label	(L)	->	residues/chains/atom	names	
	
Label	appearance:	
	
PyMOL	->	Settings	->	Label	->	Size/Font	
	
• set	label_color,		color		
• set	label_size,	10										(points,	default	is	14)	
	
To	move	label:		
	
PyMOL	->	Mouse	->	3-Button	Editing								=>	ctrl	+	left	mouse	button	
	
Clear	label:		
	
PyMOL	->	Label	(L)	->	clear	
Save	
	
Save	session:	
	
PyMOL	->	File->	save	session	(save	session	as)									(	name.pse	)	
	
Save	molecule:			save	molecule/	selection	as	pdb/cif	file	(coordinates)		
	
PyMOL	->	File->	Save	Molecule	(whole	molecule/selection)	
	
Save	image:		
	
PyMOL	->	File->	Save	Image	->	PNG	
	
	
Image	
	
PyMOL	->	Display	->	background/shadows/colors/grid/quality/reflection/…	
	
PyMOL	->	Settings	->	Label/Cartoon/Surface/Transparency/….	
	
Rendering	
PyMOL	->	Settings	->	Shadows/….	
	
Ray	button	
	
Selection	
	
• select	name												(select	RNA)	
Residue:	(resn,	r.		or	i.	)	
• select	resn		res																			(select	resn		arg)											or								select		r.	residue	
• select	resn		res+res+res			(select	resn		arg+lys	)				or								select		r.	res+res+res	
• select	resi	156-162	
Atom	type:	
• select	name	atom	type			(select	name	ca)								or							select	n.		atom	type					
	
	
	
Complex	characterisation	
Distance	measurements:		
	
PyMOL	->	Wizard	->	Measurement	
	
				pick	first	atom	=>	pick	second	atom																units:	Angströms	
	
• distance	1.	residue	number/atom	type,	2.	residue	number/atom	type					
(distance	177/O,	511/H62)	
	
	
	measurement	editing	->	A,	S,	H,	L,	C	options	
	
Find	close	contacts:	
	
• indicate	molecule/residue	4.0																										(indicate	RNA	4.0)	
	
Electrostatics:	
	
PyMOL	->	Actions	(A)	->	generate	->	vacuum	electrostatics	
	
	
Find	polar	contacts:	
	
PyMOL	->	Actions	(A)	->	find->	polar	contacts