Difference between revisions of "Jmol-Application/C4/Animation-using-Script-Commands/English"

Title Slide

Learning Objectives

For demonstration we will use models of

ethane and hemoglobin as examples.

Learning Objectives

Move, delay, slab, loop and capture.

Pre-requisites

High School Chemistry

And familiar with operations from Jmol window.

If not, for relevant tutorials, please visit our website.

System Requirement

Ubuntu OS version. 14.10

Jmol version 14.1.11

And Java version 7

Animation commands

Animation commands

delay command is used to pause a script for the specified number of seconds

Slab command is used to control the percentage of the molecule to be displayed on panel.

Animation commands

at the beginning, with an optional

time delay .

capture command captures animations as animated GIF files.

For more details on Jmol script command:

visit the web page for Jmol interactive script documentation

Create a model of ethane using modelkit menu.

Click on the hydrogen. Now we have a model of ethane on screen.

move 0 360 0 -30 0 20 0 0 5

Press enter.

The command line starts with the word move.

Followed by numbers that quantify a set of animation parameters.

Move command

move [x-rotation] [y-rotation] [z-rotation] [zoom-factor] [x-translation] [y-translation] [z-translation] [slab-cutoff] [seconds-total]

There are nine parameters in the move command.

4^th is the zoom modifier, expressed in positive or negative numbers.

Positive for zoom in and negative for zoom out.

The next three parameters deal with translation along the three axes.

It removes atoms to a specified depth so that interior features may be easily observed.

Back to the Jmol Panel.

Press up arrow key on the key board to get the previous command.

Here the delay command pauses the script for 2 seconds, before executing the next command.

move 0 360 0 -30 0 20 0 0 5; delay 2; move 0 360 0 30 0 -20 0 0 5;

Don't forget to add semicolon at the end of each keyword command.

press enter

Cursor on the panel.

We can also change the color of the atoms during this animation.

Again press up arrow key to get the previous command.

move 0 360 0 -30 0 20 0 0 5; delay 2; select hydrogen; color yellow; select carbon; color green; move 0 360 0 30 0 -20 0 0 5;

Highlight the command.

Use select key words to change the color of the hydrogens and carbons.

press enter

move 0 360 0 -30 0 20 0 0 5; delay 2; select hydrogen; color yellow; select carbon; color green; slab on; slab 50; move 0 360 0 30 0 -20 0 0 5; slab off.

Type slab off at the end of the command.

Press enter and observe the panel.

You can see parts of the molecule disappear and appear again.

Press up arrow key to get the previous command.

Type the capture command and specify the file name and path at the beginning of the command.

You can type the name of your home folder to save the GIF file.

Type,

Capture “/home/spoken-5/Desktop/sneha” move 0 360 0 -30 0 20 0 0 5; delay 2; select hydrogen; color yellow; select carbon; color green; slab on; slab 50; move 0 360 0 30 0 -20 0 0 5; slab off;

Press enter.

Open the saved GIF file with image viewer software.

Type the pdb code in the text box, 2DN1.

Press ok.

select all; color red; cartoons; select HEM; color yellow; spacefill; delay 2; slab on; slab 50; delay 1; move 90 0 0 0 0 0 0 0 4; delay 1; slab off;

We have also used move command.

The Haem part in yellow spacefill display and cut away 50% of the molecule.

Rotate 360º on X axis in 4 seconds and restore all atoms.

select all; color red; cartoons; select HEM; color yellow; spacefill; delay 2; slab on; slab 60; delay 1; move 90 0 0 0 0 0 0 0 4; delay 1; slab off; loop 2;

Press up arrow key to get the same command.

Type loop 2 at the end of the command.

"loop 2" indicates the previous script commands will be repeated after a 2 second delay.

press enter

Summary

In this tutorial we have learnt to,

Create animation of ethane and haemoglobin

using script commands such as move, delay.

We have also made use of loop and slab commands.

Saved the animations as a GIF file using capture command.

Assignment

• Take a molecule of your choice and create animation using move and delay commands.
  

• Change display, color and size of the bonds to create animation.

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