Jmol, Java Help Needed~

Question

[Hazelin]

Hey,

I am a student who needs help in my project.

I need to rotate the protein structure(from PDB) using java and the result can be seen via Jmol visualizer.

Also, I need to open 2 structures in the same visualizer to see the rotation of one structure on top of one another to calculate the RMSD. How do I get about to that?

Thank you

Your help is greatly appreciated!

Answer 1

[Tom Walsh]

The Biojava project has classes for handling protein structures. Have a look at the PDB section of the cookbook

[Hazelin]

Is Biojava a software by itself? What does it do? Because when I run it with Jcreator, it doesn't exists. Thank you for the link!

[Tom Walsh]

Biojava is a library that is used to build programs, not an application in itself.

Answer 2

[Khader Shameer]

You can automatically rotate the proteins on a JMol applet embedded in your web page using the "spin" command which renders a continuous rotation. You can implement this easily by using the Jmol.js JavaScript library

To visualized the superimposed structures on JMol you have two options:

• Load 2 structures to JMol and perform RMSD calculation for your structures and provide the results. I heard RMSD calculation is possible using JMol, but I have not yet tried this option. You could take a look at the JMol scripting options for more information about the RMSD calculation using JMol.
• Use an external program (there are many programs available, you can write on your own using BioJava or for an example you could look at a python implementation here)to calculate the RMSD and load the superposed structures to your JMol window.

I think the second option is more feasible, as I am afraid the performance of JMol depends upon the JVM settings and it may not be a good idea to superimpose structures at the client-side.

[Hazelin]

Thank you for your comment! I'm using an external program(jcreator) to write my own program and I'm having problems writing it because I'm very new to the world of Java.

[Khader Shameer]

AFAIK, JCreator is a IDE for Java. Not sure how this is affecting the integration with JMol. Please post specific issues, so that some of us can provide feedback.