Question

Programming Ramachandran Plot

1

Entering edit mode

11.0 years ago

potassiumiodide0990 ▴ 80

How do I program for Ramachandran plot in Java. Is there any module available in Biojava ? Please help

java biojava • 4.4k views

ADD COMMENT • link updated 11.0 years ago by andreas.prlic ▴ 290 • written 11.0 years ago by potassiumiodide0990 ▴ 80

0

Entering edit mode

what's your input ?

ADD REPLY • link 11.0 years ago by Pierre Lindenbaum 161k

0

Entering edit mode

a PDB file would be my input

ADD REPLY • link 11.0 years ago by potassiumiodide0990 ▴ 80

score 2 · Answer 1 · 2013-04-16

2

Entering edit mode

11.0 years ago

Ben ★ 2.0k

I'm not aware of a BioJava function but this page lists a few online tools, including RAMPAGE. The author also gives a great tutorial on drawing a Ramachandran plot in R.

ADD COMMENT • link 11.0 years ago by Ben ★ 2.0k

score 1 · Answer 2 · 2013-04-16

1

Entering edit mode

11.0 years ago

andreas.prlic ▴ 290

You can calculate Phi and Psi angles using BioJava and then plot them using your own plotting code.

ADD COMMENT • link 11.0 years ago by andreas.prlic ▴ 290