Visit-tutorial-molecular

Slides

http://ft.ornl.gov/~jsmeredith/sc10_tutorial_molecular.ppt

http://ft.ornl.gov/~jsmeredith/sc10_tutorial_molecular.pdf

Data Sets

http://ft.ornl.gov/~jsmeredith/crotamine.pdb

http://ft.ornl.gov/~jsmeredith/OUTCAR_SC10

http://ft.ornl.gov/~jsmeredith/POSCAR_SC10

Tutorial

Note: this works better with a black background and white foreground.

open crotamine.pdb

  • open crotamine.pdb (rattlesnake venom)
  • make a Pseudocolor plot of "element", hit Draw
    • note that most molecular file format readers define a variable called "element", which is the atomic number
    • the pseudocolor plot isn't very useful -- it does draw atoms as points and bonds as lines, but is treating things as continuous scalar fields
  • so delete the Pseudcolor plot, and add a Molecule plot (of "element"), and hit Draw
    • note that atoms are sphere and bonds are cylinders
    • furthermore, note that it understands that it's plotting atoms; see the legend, for instance
  • Open the Controls -> Color Table window
    • see the "cpk_jmol" color table, and turn on the "Show index hints"; note how we'll label them for you
  • close the Color Tables, and open the Molecule Plot Attributes (Atoms tab)
    • zoom in very close
    • show the quality of atoms; e.g. change to "low"
    • now change it to "sphere impostors"; note the good quality, though we're only faking spheres, so the lighting won't be perfect
    • nevertheless, make this the default for future molecule plots
    • zoom back out
    • change the radius to be based off of "Covalent radius"
    • change the scale factor to be 0.5 of covalent radius
  • go to the Bonds tab, show the various options (lines, quality, radius, color)
  • go to the Colors tab, show the color tables for various types of values
  • close the attributes window
  • change variable to resseq
  • change variable to restype
  • open the Controls -> Expressions window, and create the Scalar Mesh Variable "xc", defined as "coords(mesh)[0]"
  • change variable to xc
  • open the Controls -> Subset window, and turn off all the Hydrogens

POSCAR_SC10

delete all the plots....

  • open POSCAR_SC10
  • start to make a Molecule plot, but note there is no "Element" variable
    • this is a limitation of some file types
  • instead, make a Molecule plot of "Species"
    • note that there are two species types, just "0" and "1"
    • but we can fix this:
  • open the Controls -> Expressions window
    • we'll map species type to atomic number using the "enumerate" function
    • specifically, define "element" to be "enumerate(species, [6,8])"
  • close the Expression window, and change the variable from "species" to "element"
  • delete the element expression, and delete the plots

OUTCAR_SC10

delete all the plots....

  • open OUTCAR_SC10
  • create a Molecule plot of "element"
    • ensure sphere impostors is on
    • note it appears to be a unit cell whose orientation is not aligned to the bounding box
  • add a Mesh plot of "unitCell"
    • this is a small section which can be replicated into a super-cell
  • add the Replicate operator, open its attributes
    • check the "Use provided unit cell vectors"; the file already knows these, so we don't need to enter them
      • show big number of replications (10x and 10y, leave z at one)
      • set it back to 1x 1y 1z
      • show periodic atom replication
  • delete the Mesh plot so we can see what we're doing better
    • note that we don't have bonds; that's due to the type of file, but we can create them
  • add the CreateBonds operator, hit Draw
    • note that it hasn't done anything
    • open the CreateBonds attributes
        • maybe add a C-O bond at the top, just as an example; no C or O in this file
        • make H-* go up to 1.5 max
        • and *-* go up to 2.5 max
      • in advanced tab, show off periodic bond creation

Slides

  • annotations, high quality geometry, specular reflections
  • three-slice combining sliced charge-density grid and molecule plot
  • density contours on a slice
  • vector plot from molecular data forces
  • translucent countours
  • export to POV-Ray and ray-trace