Visualizing Your Results with VMD

CSC Spring School 2014
Visualizing Your Results
- An Introduction to VMD Michael Patzschke
University of Helsinki
The Code
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VMD – visualizing molecular dynamics
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Developed by Theoretical & Computational Biophysics Group
(University of Illinois)
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Freely available (registration necessary)
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For Linux, MacOS & Windows
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Go to http://www.ks.uiuc.edu/Research/vmd/
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Other codes: NAMD, MDFF
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Professionally developed GUI
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High quality graphics
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Scriptable
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Many useful tools
Learning Outcome
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Installing VMD
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Opening molecular structures
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Creating different representations
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Manipulating selections
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Rendering high quality graphics
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Making movies
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Scripting
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Configuring vmd
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Visualizing cube & plt files
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Saving your work
Lets See What VMD Can Do
Lets See What VMD Can Do ...
Lets See What VMD Can Do
Getting VMD
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VMD produces high quality graphical output
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Local installation preferable
After choosing the appropriate version
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Source code / Mac / Unix / Windows, w/o CUDA
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Registration (might take a day or two)
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Download ca 20MB (sources more)
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Good documentation and
tutorials available
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For tutorials:
http://www.ks.uiuc.edu/Training/Tutorials/
Installation
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Windows
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Mac
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Open the installer, rest is automatic
Open the downloaded file, put the VMD icon in the Application folder
Linux
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Unpack the downloaded file
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Change $install_bin_dir and $install_lib_dir in the “configure” file
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Run ./configure
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Enter “src” directory, run make install
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Make sure the “install_bin_dir” is in your path
Compiling from source – use programmers guide. Good luck.
Starting VMD
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Start by clicking the icon (Win & Mac) or by typing “vmd” at a terminal
Mac: add “alias vmd='/Applications/VMD\ 1.9.1.app/Contents/MacOS/startup.command' ”
to .profile (not necessary)
Look around, different windows are opened (customizable)
Configuring VMD
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Standard setting can be changed
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Look at colors
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Change appearance
This can be done in a startup file
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File “.vmdrc” searched for in
current, home, install directory
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More later (scripting)
Opening a Structure File
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VMD open 72 different formats of structure files
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Can convert a further 50 (like QC-program output)
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Pdb files will be downloaded (give four-letter code)
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Try “1GCW” (CO form hemoglobin from a spotless smooth-hound)
Manipulating the View
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Rotate molecule in display window
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left click normal rotation, right click around z-axis (Mac “cmd”+click)
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Other modes available from “Mouse” menu in main window
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Try e.g. centering the molecule
(press c in display window – click – press r to rotate)
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Press = to reset view
Try giving the molecule a spin
Different Representations
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Open the “Representation” window from Main window
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Choose different representations
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Note how the controls
change
Changing
the coloring
method
“Selected Atoms”
tool
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Try “helix” or “not helix”
or “(not helix) and
(not (not protein))
More On Selection
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See tab “Selections”
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Filters can be constructed
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Selecting a keyword shows possible values
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e.g. double-click “resname”
Double-click e.g. “ALA”
Multiple representations
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Go back to the “Draw Style” tab, write all in the atom selection
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Choose “New Cartoon” from “Drawing Method”
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Press “Create Rep”
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Write “not protein” in atom selection
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Choose “CPK” from “Drawing Method”
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Change Material (presets can be changed)
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Try changing “Rendermode” to “GLSL”
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Change resolution
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Many more representations can be added
Producing High Quality Graphics
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Rendering of images: choose “Render”
from Main Window – File menu'
Different renderers available
Tachyon will reprocess the picture,
results may be slightly different
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For the others: If window is blocked, so will be the rendered picture
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Choose Tachyon
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Add “res 1000 1000” to the Render Command
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Press “Start Rendering”
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You may want to start with smaller resolution, for
faster results
Use convert to get a jpg if needed: $>convert vmdscene.tga myname.jpg
Multiple Molecules
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Open ”File – New Molecule” from the
main window
Notice “Load files for:”
data can be loaded into existing files
Selecting “New Molecule” to load another
molecule
Main window is changed
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Change molecule name by double-click
T,A,D,F for top, active, drawn, fixed
try double-clicking to see the effect
Also available
from “Main Window Molecule”
Delete molecules here:
Scripting
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VMD contains a powerful scripting language
Available through startup-command window
or from “Extensions TK console”
Examples:
set variable value
puts $variable
expr expression
assigns value to variable
writes variable on screen
evaluates mathematical expression
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Try e.g.:
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Molecules can be selected, moved and edited with script commands
set a 2
set b 4
set result [expr $a*$b/8]
puts result
Scripting
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Information can be obtained about loaded molecules
set crystal [atomselect top "all"]
$crystal num
$crystal moveby {10 0 0}
$crystal move [transaxis x 40 deg]
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Lines and shapes can be added to molecules
graphics top cylinder { 0 0 0} { -15 0 10} radius 5 resolution 60 filled yes
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A powerful example: load the pdb files: 1fqy.pdb and 1rc2.pdb
(human and e.coli aquaporin)
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In the console do:
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Check the MolID!
Yours might be different
set sel0 [atomselect 1 all]
set sel1 [atomselect 2 all]
set M [measure fit $sel0 $sel1]
$sel0 move $M
Scripting
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The start file is a script, check this example:
Making Movies
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Trajectory files and optimization files (e.g. from TM or Orca) can be opened
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Trajectory data can be loaded into existing files (e.g. NAMD .dcd files)
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Example simple optimization
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Open movie.xyz
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Contains 43 frames
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Play optimization
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Choose frames, choose animation mode
High quality movies can be made from
“Extension – Visualization – Movie Maker”
Both trajectories or movement of a single
frame possible
Visualizing Volumes
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VMD is a good tool for visualizing cube files (e.g. densities or orbitals)
Orbitals can be visualized directly from GAMESS output files, Gaussian .log
files and molden input files
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Caveat: molden files have to be generated by molden
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Test: run a simple orca calculation
orca h2o.inp > h2o.out
orca_2mkl h2o -molden
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try opening the resulting molden file (select molden filetype in vmd)
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In “Representation” window try “Orbital”
the orbital selection is greyed out
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Now open the molden file in molden
and save it again
(molden h2o.molden.input)
Visualizing Orbitals
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Open the new molden file or take the one provided (zn_tpen.molden)
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Go to “Graphics - Representations”
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Add a new representation
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Change “Drawing Method” to “Orbital”
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Choose an orbital
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Change the isovalue
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Change coloring method
to ColorID
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Choose e.g. blue
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Add another rep
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Change isovalue to the opposite you had
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Change color to e.g. red
Visualizing Orbitals
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Try the same with the GAMESS output file provided (terpy.log)
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Some observations:
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Be sure to change the orbital
number for both phases
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Preselect the orbital range
(Orbital menu only shows 20)
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Might seem tedious, but rendered
results are very good
Mapping Cube files
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Load the provided cube file “h2o.eldens.cube”
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Into that data set load “h2o.mep.cube”
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Note the two volumes in the data set
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Go to the Representations window
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Add a representation
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Choose “Isosurface” as drawing method
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Change “Coloring Method” to “Volume”
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Change “Draw” to “Solid Surface”
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Change “Show” to “Isosurface”
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Choose eldens.cube as the volume
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Choose mep.cube to map
Mapping Cube files
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Go to the tab “Trajectory”
Change “Color Scale Data Range”
to get a good result
Color scale can be changed in
“Graphics – Colors” (Main Window)
Slicing a Cube
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Choose “Volume Slice” as drawing method
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Choose “Throb” as coloring method
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Slice at different points using “Slice Offset”
Other Things To Try
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Use online tutorials
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Play around
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Look at the “Extensions” Menu in the Main Window
Have fun!
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Thank you for your attention