load $glucose; spin 30 # the value refers to the rotation speed6 - Some animations with Jmol
Objectives:
1. Understand a molecule animation as a script
2. Use the molecule animation console
1 Animate the molecules.
And we have reached the last part of the Course with Jmol, to present a very interesting educational effect of the program: molecule animation.
You may want to show a molecule with different styles during a certain period, or make a slow transition between colors in specific atoms, or even controlled enlargement, reduction, or rotation effects. And many others that your imagination and technical rigor allow you to study.
In these cases, it is interesting to know and apply a few animation commands explained below. The examples have been selected to simplify each command. But don’t be fooled by the capabilities of Jmol, because for each command there are always several complementary options. And if you want to know anything about any Jmol command, visit the reference website.
1.1 Spin
Simple command to rotate the molecule.
1.2 ZoomTo (resize)
This command is impressive because it allows for controlled magnification or reduction over time. Its syntax is:
*zoomTo* : time (optional expression) sizeExamples:
Increase by 3x, half a second at a time: zoomto 0.5 *3
Increase by 4x, half a second at a time: zoomto 0.5 400
Focus on a biopolymer ligand with 2x magnification: zoomto 2(ligand) 0
Focus on a biopolymer ligand with 4x magnification, half a second at a time: zoomto 0.5(ligand)* 41.3 Delay
This is a key command for any animation, as it allows the image of the molecule in Jmol to pause (in seconds) before the next action. It is normally used in the sequence of commands by the Console throughout a script.
delay 3 # waits 3 seconds before the next actionWe can try out an animation with the above commands using the cyclohexanol model.
Here is a code snippet for you to try out animations with Jmol. Just copy and paste it into the Console and run it. If you prefer to make any changes, it is best to copy it to a notepad, modify it, and test the script in the Console.
Now it’s up to you:
load $cyclohexanol
delay 2
spin Y 70
delay 2
spin off
zoomTo 2 *2
cpk
delay 2
color transparent
zoomTo 2 *0.5
spin 50