test_page

Status: test page — not a lesson, never published

In this lesson you will see every component a lesson page can use, once each, so one paste into Drupal and one accessibility scan cover them all. Time: 5 minutes · Branch: Testing · Program: any · Also in: a real lesson

About this page
Before this Data You'll need
The lesson map homo.cube, from the orbitals lesson Nothing else

Why this matters

Lesson pages use about a dozen building blocks: callouts, steps, code, figures, answers you can open, tables and links onward. If each one survives the editor and passes the scanner here, every lesson made of them will too. The same idea works for any cube file you convert.

Callouts

Note

A note: extra context the reader can skip.

Tip

A tip: a faster or better way.

Important

Important: something that goes wrong if skipped.

Warning

A warning: risk of lost work, wasted allocation or a wrong result.

Steps

Step 1: Run a command

Run in: the OnDemand desktop terminal

python ~/ama27-curriculum/tutorials/visualization/scripts/make_cubes_pyscf.py --out ~/scratch/cubes --grid 80 --check

You should see:

check: 4 atoms; density integrates to 15.917 electrons (expect 16) -> PASS

Step 2: Type in a program

Type in: the ChimeraX command line

volume #3 level -0.02 color blue level 0.02 color red style surface

You should see: blue lobes and red lobes around the molecule.

A figure

Formaldehyde's HOMO in the plane of the molecule: lobes of opposite sign on either side of the oxygen, and around each hydrogen.
Figure 1. The highest occupied orbital of formaldehyde, in the plane of the molecule. Red is positive and blue negative; solid and dashed lines mark +0.02 and −0.02.

A diagram

Diagram: From calculation to picture. A calculation writes a cube file, a program reads it, and an isosurface turns it into a picture.

Check your understanding

Why does an orbital need two isosurfaces?

Its values are positive in some regions and negative in others, so one surface goes at +0.02 and one at −0.02.

Where does the text of this answer go when the page is printed?

Onto the paper: the optional script step opens every answer just before printing.

If something goes wrong

If something goes wrong
What you see Why What to do
A callout has lost its label The editor removed a class Reopen the page in Source mode and compare with this file
A long command wraps onto two lines Section 35 of the stylesheet is missing Paste sections 31–38 into the custom block

Next

Credits

Figure made from the orbitals lesson's homo.cube with make_sampler_figure.py. Written for SBSC; text CC-BY 4.0.