Transcript Slide 1

 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 nonprotein 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, e.g.
show spheres, resi 1
commonly used commands
more in PyMol docs @ http://www.pymolwiki.org/
Pymol

download 1PD8, 1PD9 and 1PDB in PDB format

load them into Pymol as objects
log_open log.pml
load 1PD8.pdb, ter
load 1PD9.pdb, bi
load 1PDB.pdb, apo

Alignment
align ter, apo
align bi, apo


-
PDB files having ss from programs like DSSP
PyMOL has reasonably fast ss assignment using dss
selection
To change assignments manually, the best way is to use
the alter command as follows:
show cartoon
alter 40-52/, ss='L'
alter 52-65/, ss='S'
alter 65-72/, ss='H'
rebuild # regenerate
# assign residues 40-52 as loop
# assign residues 52-65 as sheet
# assign residues 65-72 as helix
the cartoon
Pymol

download 1PD8, 1PD9 and 1PDB in PDB format

load them into Pymol as objects
log_open log.pml
load 1PD8.pdb, ter
load 1PD9.pdb, bi
load 1PDB.pdb, apo
Alignment
align ter, apo
align bi, apo

Alter Secondary structure
alter (ter and (resi 59-60), ss='L'
rebuild

 Object (ter, bi and apo)
 Show car, ter
 Select 1, resn ALA
 # Select backbone
and name N
nitrogens from
alanine residues
 Show spheres, 1
 Select 2, resi 1:20
 #select residues 1-20
 Show sticks, 2
 select 3, elem O and not name OH
 # Select all oxygen atoms except
hydroxyls
property
symbol
short example
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, resn
asp+glu+asn+gln
resi
i.
residue numbers, select mults10, resi
1+10+100+1000
chain
ss
c.
-
chain ID
secondary structure type, select
allstrs, ss h+s+l+""
 and, or, not
etc.
 how would you select resid 27 and resid
28?
property
short
example
not s1
and
or
! s1
&
|
atoms that are not included in s1
atoms included in both s1 and s2
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
example
s1 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
Expands selection to complete residues
br. s1
select cmplt, byres near10
neighbor s1
nbr. s1
atoms directly bonded to s1
select vic, nbr. resi 10
s1 extend X
s1 ? X
Extends s1 by X bonds connected to atom in s1
select 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 equivalent
select (name cb or name cg1 or name cg2)
and chain A
select name cb+cg1+cg2 and chain A
# PyMOL will expand its logical selection out
# from the innermost parentheses
byres ((chain a or (chain b and (not resi
125))) around 5)



1.
2.
3.
4.
5.
6.
select residue 301 in ter (name it CO4)
Pymol
show it as stick, zoom at it
Save this selection as molecule in file co4-1.pdb
select CO4, (ter and resn CO4)
show stick, CO4
Save co4-1.pdb, co4
load co4-1.pdb, co4 #create new co4 object
Show surface, co4
show sticks, byres ((ter and ((resn CO4) x; 3.5)))





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
disable, enable
1
 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
2
# EXAMPLE 1: Show hydrogen bonds between protein
# and
ligands (which must have hydrogens)
load 1PD8.pdb,ter
CO4 as a ligand
h_add ter
select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor
hydro)))
dist HBA, (co4 and acc),(ter and don), 3.2
dist HBD, (co4 and don),(ter and acc), 3.2
delete don
delete acc
hide (hydro)
hide labels,HBA
hide labels,HBD
1.
2.
3.
4.
5.
6.
h_add ter
select HD, (elem n,o and (neighbor hydro))
select HA, (elem o or (elem n and not
(neighbor hydro)))
dist HBD, (co4 and HD), (ter and HA), 3.5
#distant name = (selection1), (selection2),
cutoff distant (selections are in the same obj)
dist HBA, (co4 and HA), (ter and HB), 3.5
dist X, (ter and (resi 301 and name; C5')), (ter
and (resi 31 and name; CE2)), 4.5
 bg
white
 set bg_rgb, [120, 12, 30]
 set dash_width, 5
 set dash_radius, 10
 label (resi 301 and name; o3'), "CO4"
 label (resi 31 and name; CA), “Phe31”
 set label_font_id, 10
 set label_color, red
 PyMOL
script – text file with commands,
each at one line
 *.pml
 useful feature: get_view command
 run script from PyMOL: @log.pml
 or from command line as
pymol aaa.pml
 save the image
•ray
•png