Download The Basics of UCSF Chimera

Chem
240
Fall
2011
1
The
Basics
of
UCSF
Chimera
This
is
a
very
basic
introduction
to
UCSF
Chimera,
a
powerful,
free
software
package
for
visualizing
and
analyzing
macromolecules.
If
you
want
to
explore
Chimera
further
after
running
through
this
tutorial,
check
out
the
Chimera
user’s
guide,
at:
www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html
To
begin,
download
and
install
the
latest
production
release
of
UCSF
Chimera
(currently
1.5.2):
www.cgl.ucsf.edu/chimera/download.html
___________________________________________________________________________
Part
One:
Loading
structures
and
basic
viewing
Open
Chimera.
Chimera
can
read
several
file
formats,
including
PDB,
or
“Protein
Data
Bank”.
The
PDB
is
a
collection
of
structural
data
on
proteins
(and
other
biomolecules)
and
can
be
found
online
at
rcsb.org.
It’s
awesome.
Any
one
of
the
63,000+
structures
on
the
pdb
can
be
downloaded
directly
into
Chimera
if
you
know
the
pdb
code.
For
this
exercise
we’ll
use
a
structure
of
insulin,
pdb
code
3i3z.
Here’s
how
to
load
it
in
Chimera:
From
within
Chimera…..
Go
to
File/fetch
by
ID
Type
in
3i3z
and
click
“Fetch”
After
a
moment,
a
structure
will
appear
on
the
screen.
This
is
the
peptide
hormone
insulin.
Take
a
moment
to
familiarize
yourself
with
the
controls.
To
rotate
the
molecule,
left‐click
and
drag.
To
zoom
in
and
out,
right
click
and
drag
OR
use
the
scroll‐wheel
To
translate
the
molecule
in
the
plane
of
the
screen,
using
a
3­button
mouse,
middle‐click
and
drag
On
a
Mac,
or
on
a
PC
without
a
middle‐mouse
button,
we’ll
have
to
change
the
default
controls:
Favorites/preferences
Category:
Mouse
For
the
translate
x,y
column,
click
the
Ctrl­2
button,
as
shown
below:
Chem
240
Fall
2011
2
Click
Here
Now
you
can
translate
in
the
x,y
plane
by
holding
“CTRL”
on
the
keyboard
and
right
click‐dragging
with
the
mouse.
There
are
a
lot
of
options
available
from
the
menus
on
the
top
of
the
window.
Still
more
are
available
through
the
command
line,
which
you
should
enable:
Favorites/Command
line
The
bottom
of
the
window
should
expand
to
reveal
the
word
“Command:”
with
an
empty
space
next
to
it.
The
command
interface
can
be
very
powerful,
enabling
you
to
even
script
your
own
molecular
movies.
But
right
now,
I
only
want
you
to
remember
one
command:
focus
When
you
type
focus
in
the
command
line
and
hit
enter,
it
brings
the
molecule
back
into
the
center
of
the
screen.
Very
useful
if
you
get
lost
while
rotating
and
translating.
Answer
the
following
questions
and
email
them
to
your
instructor.
Chem
240
Fall
2011
3
Part
2:
Visualizing
Insulin
You’re
looking
at
the
protein
in
ribbon
form,
in
which
a
ribbon
traces
out
the
backbone
of
the
protein.
Notice
that
if
you
hold
your
mouse
over
any
part
of
the
structure
and
wait
for
a
second,
a
window
pops
up
with
information
about
what
is
directly
under
your
pointer.
Hold
it
over
a
part
of
the
protein
and
you’ll
see
the
3‐letter
code
for
the
amino
acid
at
that
spot
along
with
its
sequence
#
and
chain
ID.
This
structure
has
two
chains,
so
depending
on
where
you
hover
your
mouse
you
might
see
info
on
an
amino
acid
from
chain
A
or
chain
B.
Using
this
technique,
answer
these
questions:
(1)
What
is
the
first
amino
acid
of
Chain
A?_________________
What
is
the
last
amino
acid
of
Chain
A?_________________
What
is
the
first
amino
acid
of
Chain
B?_________________
What
is
the
last
amino
acid
of
Chain
B?_________________
Now
let’s
turn
on
the
side
chains:
Actions/atoms­bonds/sidechain­base/show
The
backbone
is
still
treated
as
a
ribbon,
but
now
the
sidechains
should
be
projecting
outward.
The
command
line
can
be
used
to
select
individual
residues,
either
by
sequence
number,
or
amino
acid
type,
etc.
Type
this
in
the
command
line:
sel
:29.B
Press
enter.
An
amino
acid
should
become
outlined
in
green.
What
residue
was
selected?
Give
the
full
name,
3‐
letter
abbreviation
and
one‐letter
abbreviation:
(2)
____________________________________________
Control
click
outside
of
the
molecule
to
unselect.
Chem
240
Fall
2011
4
The
default
display
for
atoms
in
Chimera
is
“stick”,
which
is
great
for
seeing
the
geometry
of
a
molecule,
but
not
so
great
for
getting
an
idea
of
how
much
space
an
atom
occupies.
Try
out
the
various
other
display
options
for
atoms
and
bonds:
Actions/atoms
bonds
(and
then
choose
either
wire,
stick,
ball
and
stick,
or
sphere)
Note:
as
you
do
this,
remember
that
the
backbone
atoms
are
still
hidden…the
backbone
will
stay
as
a
ribbon
as
the
sidechains
change
their
appearance.
As
you’ll
see,
sphere
displays
atoms
based
on
their
Van
Der
Waals
radii,
which
is
a
good
approximation
of
an
atom’s
size.
Switch
to
sphere
mode.
Comment
on
the
colors
of
spheres
in
this
depiction:
(3)
What
does
red
signify?_______________
Blue?_______________
Grey?________________
Yellow?_________________
Comment
on
the
distribution
of
colors
in
the
structure.
Are
non‐grey
atoms
found
evenly
distributed
throughout
the
structure,
or
are
they
mostly
on
the
inside
or
outside?
Explain
the
sensibility
of
your
observation
in
terms
of
water
solubility.
(4)
Are
there
any
hydrophobic
patches
on
the
exterior
of
insulin?
If
so,
give
an
example
of
a
specific
amino
acid
in
this
patch,
including
its
sequence
number
and
chain
ID.
(5)
Switch
back
to
stick
view.
Take
a
close
look
at
the
yellow
bonds
that
connect
the
two
chains
of
insulin.
What
types
of
bonds
are
these,
and
how
many
of
them
exist
in
this
structure?
(6)
Chem
240
Fall
2011
5
Lets
finally
take
a
look
at
the
shape
of
the
whole
protein.
To
do
this
we’ll
use
the
surface
command,
which
is
like
putting
shrink‐wrap
over
the
spheres
that
represent
each
atom
in
the
molecule.
This
is
probably
the
best
way
to
get
an
idea
of
the
overall
shape
of
a
protein,
including
binding
pockets
and
crevices.
Actions/surface/show
Move
the
structure
around
a
little.
You’re
looking
at
the
solvent‐accessible
surface
area
of
the
protein.
In
other
words,
the
parts
of
the
protein
that
water
can
“touch”.
Notice
all
the
blue
and
red!
In
this
depiction,
the
surface
is
colored
by
atom
identity;
that
is,
if
an
atom
is
carbon
it
gets
one
color,
if
its
oxygen
it
gets
another,
etc.
We
actually
have
lots
of
coloring
options
in
Chimera
to
help
us
see
patterns
in
a
molecule…one
useful
approach
is
to
color
by
the
hydrophobicity
of
each
amino
acid.
There’s
a
shortcut
for
this
one:
Presets/interactive
3(hydrophobicity
surface)
Here
orange
is
hydrophobic,
blue
is
hydrophilic
and
white
is
considered
in
between
the
extremes.
Notice
that
big
hydrophobic
patch
again.
Insulin
in
its
inactive
form
is
a
hexamer.
The
hydrophobic
patch
helps
it
to
clump
together
to
form
these
larger,
6‐member
complexes.
To
make
the
surface
slightly
transparent
so
we
can
see
the
backbone
ribbon
inside,
Actions/Surface/Transparency/70%
(or
some
other
%...play
around
a
bit)
Save
an
image
of
this
scene
and
email
it
to
your
instructor
along
with
the
answers
to
the
questions
above.
To
save
an
image:
File/save
image/Save
as/save
The
default
image
options
are
fine.
A
final
note
on
saving
work:
You
save
your
work
in
Chimera
as
a
“session”.
Its
not
required
for
this
exercise,
but
here’s
how
to
do
it:
File/Save
Session
As…
Note
that
if
you
want
to
reopen
a
Chimera
session,
you
can’t
double‐click
the
session
file
like
you
would
a
word
document.
You
have
to
first
open
Chimera,
choose
File/open
from
within
Chimera
and
then
navigate
to
the
session
file
(it
will
have
the
extension
.py).