Macromolecule
analysis with vmd
Shy Arkin
[email protected]
Thursday, July 2, 2009
Visual Molecular Dynamics
• One of the best programs to (dynamically)
analyze and visualize macromolecules.
• Free from Klaus Schulten’s group at:
www.ks.uiuc.edu/Research/vmd/
• Available for virtually all platforms.
• Do not expect messages such as:
“are you sure you want to...”
• Do not expect undos.
Thursday, July 2, 2009
Comparable Programs
• Only one - Pymol (www.pymol.org).
• PyMol may be better for visualization in
terms of the final image quality (surfaces
and transparency in particular).
• However, for analysis and definitely for any
dynamical analysis vmd is much better.
Thursday, July 2, 2009
GUI vs. command line
• vmd contains an extensive GUI with lots of
options and analysis packages (help is
minimal however).
• It has a command line (unix shell) interface
in which you can do everything that you
can do in the GUI and (much) more.
Thursday, July 2, 2009
vmd and Tcl
• vmd has Tcl, an embedded scripting
language in it, that allows you to do
practically anything that you can think of.
• This will be the subject of the next session.
• There are also vmd versions with Python as
the embedded language, but it is less
powerful (at least for now).
Thursday, July 2, 2009
Online vmd tutorial
• www.ks.uiuc.edu/Training/Tutorials/vmd/
tutorial-html/
Thursday, July 2, 2009
running thru vmd...
• Loading a Molecule
• Displaying the Protein
• Exploring Different Drawing Styles
• Selections
• Images and (simple) movies
• Defaults (vmdrc)
• Saving your Work
Thursday, July 2, 2009
Loading a molecule(s)
%> mol load pdb 1ZCD.pdb
Thursday, July 2, 2009
Different windows
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vmd main
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Molecule ID
Top
Animate
Display
Freeze.
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open GL
terminal
TkConsole (later)
Perspective vs
Orthographic
• You can change the from Perspective to
orthographic from the display menu.
• You can change the annoying default of
Perspective to orthographic in the vmdrc
file.
%> display projection orthographic
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Movement
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r - rotation
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c - center
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t - translation
s - scale (scrolling does
the same)
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right click rotates about
an axis
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“=” will put your rep in
the screen.
Simple measurements
1. selects an atom
2. select 2 atoms to measure a distance
3. selects 3 atoms to measure an angle
4. select 4 atoms to measure e a dihedral.
5. You can delete/hide the labels in the
graphics ➝ labels palette.
Thursday, July 2, 2009
Drawing styles
(a) The representations
(b) Selection
(c) Coloring method
(d) Drawing method
Thursday, July 2, 2009
Visualizations
• Changing colors and materials
• Labels
• Visualizations extensions
• Cloning representations
• Clipping planes
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Sequence viewing
• Very useful to
quickly glance at
your structure
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Selections
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Selections can be made
either directly or by the
GUI (double click).
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They can be defined in a
macro in your .vmdrc
file (later).
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They can be ridiculously
complex and powerful.
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Boolean operators work
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Thursday, July 2, 2009
Normal shell tricks
work (e.g. ctr-u, ctr-a,
ctr-e) as do copy and
paste.
Use parenthesis
Wild cards (regex)
Case sensitive
Example selections
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Thursday, July 2, 2009
name CA
resid 35
resid 35 50
resid 35 to 50
index 50
name CA and resname
ALA
backbone
not protein
noh
within 5 of name FE
same residue as name C
name 'A 1'
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name "C.*"
mass < 5
numbonds = 2
abs(charge) > 1
x < 6 and x > 3
x^2 + y^2 +z^2 < 300
protein within 5 of nucleic
same resname as (protein
within 5 of nucleic)
protein sequence "C..C"
name eq $atomname
protein and @myselection
Images
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Several different rending
approaches.
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In our experience povray
(a free ray tracing program) is
the best:
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Thursday, July 2, 2009
Make a .pov file.
Use povray to render.
It can then be changed
www.povray.org
(or as big as you would like it)
Thursday, July 2, 2009
Transparent background
• Adding an alpha channel will do it. If you want to
force is do as follows:
• In the povray file change (extra lines or spaces
don’t mater):
background {color rgb<0.000, 0.000, 0.000>}
• to:
background {color rgbft<0.0,0.0,0.0,0.0,0.0>}
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Simple Movies
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A movie means lots of images that are used to make a
movie.
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You can use your own program to join the images to a
movie (e.g. Quicktime pro) or uses vmd’s default
(later).
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You can do simple and reasonable movies with the GUI
(extensions ➝ visualizations movie ➝ maker).
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You can make far better movie using simple scripts
(later...).
Thursday, July 2, 2009
Movie settings
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Chose the rendering engine.
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Get netpbm at: netpbm.sourceforge.net
Thursday, July 2, 2009
Set the correct directory for the files.
Deselect delete image files!!!!
This can take a (very) long time.
You might need to convert the ppm images to jpg
before using quicktime.
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“simple” analysis
with vmd GUI
• Measuring distances, angles and dihedrals
(see above).
• Measuring RMSD.
• Ramachandran plots.
• Electrostatics analysis.
• Radial pair distribution function (RDF).
Thursday, July 2, 2009
RMSD
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Load an additional
structure.
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Then align and calculate
the rmsd.
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Try cloning the
representation.
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The alignment and
calculation is relative to
the “top” molecule.
Use rmsd calculator
from the analysis menu.
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This of course can be
changed.
You need to select the
same number of atoms.
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You can save the aligned
molecule coordinates by
right clicking.
Thursday, July 2, 2009
Ramachandran plots
• Extensions ➝ Analysis ➝ Ramachandran.
• You can select whichever residues you like.
Thursday, July 2, 2009
PME electrostatics
• You need to assign the charges of every
atom in the system.
• A good way to do this is to have a pqr file
which is a pdb with the charges in the beta
column.
• Use pdb2pqr if you don’t have the charges
(pdb2pqr.sourceforge.net).
Thursday, July 2, 2009
PME electrostatics cont.
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You need a neutral
system.
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Make sure you know
the size and origin of
your system.
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Set the parameters
as follows.
Thursday, July 2, 2009
Radial pair distribution
• Extension ➝ analysis ➝ Radial pair
distribution.
• It is very easy to calculate the RDF of any
two selection, just don’t forget to set the
unit cell size.
Thursday, July 2, 2009
Salt bridges
• Extension ➝
analysis ➝ salt
bridges.
• The output is a
text file.
• Play around with
the parameters.
Thursday, July 2, 2009
Manipulations
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By clicking a number you
can move stuff
permanently, i.e. no
undo!
The coordinates can
then be saved by rightclicking the structure.
5. move atom
6. move a residue
7. move a fragment
8. move a molecule
9. move the highlighted
representation
Thursday, July 2, 2009
.vmdrc
• Put all your defaults in a file that vmd reads
in a file called:
• .vmdrc in mac and linux
• vmd.rc on a PC
Thursday, July 2, 2009
# simple defaults
display projection orthographic
axes location off
color Display Background white
# position and turn on menus
menu main move 5 196
menu display move 386 90
menu animate move 124 7
menu edit move 125 196
menu graphics move 5 455
menu files move 5 496
menu mol move 5 745
# macro selections
atomselect macro hydroxyl {(resname SER THR and name OG OG1 HG HG1)\\
or (resname TYR and name OH HH)}
menu main on
Thursday, July 2, 2009
Saving your work
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You can save (and then
load) the state of what
you have done.
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However, any rotations/
scaling that you do the
the pdb are not saved.
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These can be done via
the command line.
Thursday, July 2, 2009
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If you changed the
coordinates then right
clicking a structure can
save you its coordinates.