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