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