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Pymol Commands Gates PDF
Pymol Commands Gates PDF
Pymol Commands Gates PDF
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.
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
Setting→Cartoon→Side
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)
•
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
(coloring
carbons
gray
helps
me
because
I
can’t
see
yellow
sulfurs
against
the
green
default
color
that
Pymol
uses
for
carbons)
• 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
•
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)”.
•
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).
•
Size
of
spheres
can
also
be
changed
(0-‐1):
set
sphere_scale=0.5
(I’m
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,
I’m
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
Å
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
sticks
and
balls
will
be
the
same
color.
If
different
colors
are
desired,
this
can
be
achieved
by
creating
separate
objects
for
each.
•
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 Å
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
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.
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:
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.
In
3-‐button
editing
mode,
double-‐click-‐and-‐hold
on
the
atom…
then
drag
it
where
you
want
it!
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
In 3-‐button editing mode: left-‐click on an atom then hit “Crtl-‐D”
In
3-‐button
editing
mode,
select
a
hydrogen
atom
by
left-‐clicking
on
it,
then
hit:
“Crtl-‐C”…this
adds
a
CH3
group.
Then,
select
a
hydrogen
atom
on
the
end
of
the
growing
chain
and
hit
Crtl-‐C
again,
etc.
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:
(b) shift-‐right click moves it “in and out” on z-‐axis
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.