How this tutorial works

This frame contains a scrollable list of modifications you can make to the molecule on display in the frame to the right. Click on the the small 'x' button next to the description of a change to execute the corresponding script. Click on its 'How to' button to see the source code behind the command and the '?' button for an explanation of what is being done to the molecule. 'How to's and explanations appear in the frame directly beneath the structure.

Note: general format of each 'x' button is:

<embed type="application/x-spt" width=12 height=12 button=push target="struct" script="____">

Hint: If the display becomes unrecognizable, select "(Re)load 'Antimycin3.pdb'" to restore it to its initial state.
Display as spacefilling (using default radius)  
Display as spacefilling (using radius = 500)  
Display molecule as wireframe  
Rotate 90 degrees about X  
Rotate 90 degrees about Y
Rotate 90 degrees about Z
Translate to X = +2
Translate to X = -2
Translate to X = 10
Translate to Y = 5
Note: Translations along the Z axis are not available; see 'Zoom' below
Translate to X=0, Y=0
Set (CPK) radius to 250 (==1.0 Angstrom)
Set (CPK) radius to 2 Angstroms
Set solvent off
Set ambient lighting to 20%
Set ambient lighting to 50%
Set ambient lighting to 100%
Display using specular highlights
Display without specular highlights
Display axes
Hide axes
Display bounding box
Hide bounding box
Display as ribbon
Wireframe w/o Ribbon
Zoom 200%
Zoom 400%
Zoom 100%
Zoom ON
Zoom OFF
Display dot surface
Hide dot surface
Highlight atom 1
Highlight atom 10
Highlight atom 100
Highlight all atoms within 5 Angstroms of atom 7
Highlight all nitrogens
Highlight all oxygens
Highlight nothing
Color molecule gray
Set molecule black
Color molecule according to CPK scheme
Color background gray
Set background to black
Set background white
Color background purple
(Re)load 'Antimycin3.pdb'
Load 'big2.mol'
Load PDB file
Clear the structure box
Note: options involving hydrogen bonds only apply to data sources containing hydrogen bonding information, such as PDB files.
Display hydrogen bonds
Hide hydrogen bonds
Restore molecule to initial size and orientation
Shadowing On
Shadowing Off
Atom labels on
Atom labels off
Use 4 pt. font
Use 8 pt. font
Label atoms with sequential numbers
Copy to clipboard (as graphic)


A summary of these commands is available as a handy, printable page.