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cornawakeΛογισμικό & κατασκευή λογ/κού

4 Νοε 2013 (πριν από 4 χρόνια και 6 μέρες)

135 εμφανίσεις

Introduction to Pymol


http://www.pymol.org

http://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)

A
ction

Navigation

Quick draw

Manipulation

S
how

H
ide


same content as
Show


Use Show and
Hide to toggle
things on and off

L
abel

C
olor


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/OH


Selector: selection "sele" defined with 12 atoms.


This could be read as “you clicked atom OH which
is on the 322
nd

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 1
st

argument is specific to
command used, while the 2
nd

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.pd
f



download 1GBV in PDB format


load it into Pymol as 1gbv object



help show

load 1gbv.pdb, 1gbv

hide

show cartoon

hide cartoon, chain A

show ribbon, chain A

set ribbon_width, 5

hide cartoon, chain B

show spheres, chain B

hide cartoon, chain C

show sticks, chain C

color red, chain A

color blue, chain B

color 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 A


color red, sele


color 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 42


show 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 10

zoom 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
s
1

and

&

atoms included both

in
s
1 and

s
2

or

|

atoms included in either

s
1 or

s
2

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

s
1

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 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


s
elect (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


P
yMOL 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 dots


select 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