Visualization

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Overview

  • See Fundamentals of Data Visualization for a nice introduction to data visualization and techniques for visualizing different types of information.
  • Molecular visualization
    • Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. Useful for quick inspection of structure and trajectories.
    • OVITO: a scientific data visualization and analysis software designed for molecular and particle-based simulation models.
    • VESTA: a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Convenient to use with VASP.
    • Multiwfn: a very powerful program for electronic wavefunction analysis (e.g., charge density, ELF, ESP, NCI, and orbital fields).
    • VMD: a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
    • PyMol: a molecular visualization system for rendering and animating 3D structures.
  • Structure editor
    • Avogadro: a free and open source molecular editor and visualization tool.
    • Materials Studio
    • Schrodinger
    • Aten: a molecular modelling package that allows editing and manipulation of atoms and molecules in isolated and periodic systems, and offers full editing via either graphical user interface or command line (scripted) operation.
  • 3D visualization
    • ParaView and VisIt are two general purpose visualization tools, which support volume rendering and other advanced techniques.
    • VTK is an open-source C++ library for 3D computer graphics, image processing and visualization, and has several interpreted interface layers including Tcl/Tk, Java, and Python.
  • 2D plotting

Materials Studio

  • Ask a group member if you need to use this.
  • From the Help -> Help Topics menu, you can find a list of help topics and tutorials. I recommend going through “Tutorials > Visualizer tutorials” and “Materials Studio interface > Mouse and keyboard actions”.
  • Browse “Sketching and editing structures”, “Visualizer Tools”, and “Building Tools”. Familiarize with its capability and come back to these topics when you use them.

Count atoms in a unit cell

  1. Right Click -> Display Style -> Lattice Tab -> Style: Original
  2. Edit Menu -> Atom Selection -> Select by Property: Element, Selection Mode: Create a new selection -> Select

Schrodinger

  • Obtain the required software license files through your institution or the software vendor before installation. Follow their licensing terms and keep the license files private.
  • Download and install Schrodinger.
  • After installation is complete, start “Configure Software” and add the two .lic files extracted from Schrodinger_licenses.zip.
  • You can now launch Materials Science (use this instead of Maestro).

NOTE: For licensing to work in the last two steps, your IP needs to belong to the University network, so use VPN if you’re not on campus. After the program is started, you can disconnect from VPN.

  • From the Help -> Tutorial menu, you can find a list of tutorials and click View to see it in browser. I would recommend going through “Introduction to Maestro for Materials Science”.

VMD

Installing VMD

  1. Go to the website. Click on the VMD button and find your platform (preferably with Open GL). Click to begin the download.
  2. Follow the instructions to create a user account (used to determine usage and reported to the NSF or other funding agency supporting VMD development) and browse the README file (onscreen) while the program downloads.
  3. When download is complete, open a Finder window and move VMD into the Applications folder. To do this, drag the VMD icon (looks like a water molecule) over the ‘Applications’ menu on the left of the Finder window. The cursor should become a green plus sign.

Generating high-quality images

  • Make sure that in the Graphical Representations window, all your visualized components have high values for their resolution.
  • Open File Render Controls: from VMD Main window, File -> Render.
  • Changing the method from “Snapshot (VMD OpenGL window)” to basically anything else will dramatically improve the image quality. VMD User’s Guide recommends “Tachyon (internal, in-memory rendering)”. The default Snapshot renderer just captures what is on the VMD OpenGL Display area. It will even include other objects that are on top of the display window at the time when you perform the rendering.
  • To use renderers other than “Snapshot (VMD OpenGL Window)” or “Tachyon (internal, in-memory rendering)”, you need to perform two steps: first generate a scene description file from VMD, and second run the separate rendering program with your desired options to generate a raster graphics file. See Chapter 8.2 Higher Quality Rendering of VMD User’s Guide for more details on the different rendering programs and recommended options.
  • For example, to use Tachyon renderer with custom parameters, choose “Tachyon”, and in the Render Command text box enter: “/Applications/VMD 1.9.1.app/Contents/vmd/tachyon_MACOSXX86” -aasamples 8 -rescale_lights 0.4 -add_skylight 0.7 %s -format TARGA -o %s.tga. VMD will generate a scene file suitable as input for the Tachyon rendering program, with the name specified in the Filename text box, and then run the command given in the Render Command box to actually render the image. “%s” is the file name specified in the Filename box.
  • In addition, you can manually modify the scene file in order to change settings such as the resolution, anti aliasing threshold, and re-run the rendering program from the command line to generate another image file with the modifications you just made to scene descriptions.

Add/remove bonds

When reading in a simulation snapshot, VMD will try to determine the bonds between atoms. Sometimes it will draw bonds where they should not exist and at other times it can also miss certain bonds. Use the pickbond script from VMD Script Library to add/remove bonds.

  • Save the file to your disk.
  • Open VMD Main Window -> Extensions -> Tk Console.
  • Change to the directory where you save the tcl script and invoke the script:
cd target/directory
source pickbond.tcl # read in the script
pickbond add/del/stop # add bond, remove bond, stop pickbond action
  • Change the mouse mode to Pick by pressing P or from VMD Main Window -> Mouse -> Pick.
  • Click the two atoms between which you want to create and delete a bond.

Perform periodic boundary conditions at arbitrary positions

Sometimes you will want a particular molecule to be at the center of your system while your movie file has it always at the boundary of the simulation box. Suppose the simulation box is cubic with sides of length 32.0, and the molecule of interest is at (16.0, 32.0, 0.0), you can do the following:

set sel [atomselect top "all"] # select all atoms in your top molecule
$sel moveby {0 -16 16} # move all molecules
pbc set {32.0 32.0 32.0 90.0 90.0 90.0} # set the lattice parameters of the simulation box
pbc wrap # perform periodic boundary conditions
pbc join connected # re-connect molecules

ChemDraw

  • Start by selecting an appropriate template: File -> Apply Document Settings from -> ACS Document 1996.
  • Arrange drawings properly with respect to the page/column width or whatever is the desired final figure width. Do not scale pasted image in Word or LaTeX; otherwise the font and symbols will not be of the right size.
  • Select new objects you draw and try auto-adjusting bond lengths and angles: Structure -> Clean Up Structure.
  • To add labels, right select the structure and click Analysis -> Structure, which will create an auto-aligned label below the structure. You can then edit the label. This will stop auto-updating. Labels created this way will not have warnings about wrong valency, etc. Alternatively, right select labels created using Text tool and uncheck Interpret Chemically.
  • Make sure the schematic makes sense. For example, if you have a two-step reaction: A + B <-> C and then C + D -> E, do not draw A + B <-> C + D -> E. Instead, introduce D using a half arc above the second arrow.
  • See this video on how to quickly draw a catalytic cycle and a few handy tips.

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