My software notes

April 6, 2013

Morphing movie using RigiMOL/PyMOL

Filed under: pymol/ molmol — kpwu @ 2:14 am
Tags: , ,

RigiMOL is a feature only available in incentive PyMOL, not in open source built PyMOL.

The following two short (very short) youtube videos are made by the example script provided at PyMOLWiki (script link at here).

The demo script is also pasted at here:

====================================

# get open and closed conformation of adenylate kinase

fetch 1ake 4ake, async=0

# make two state object

align 1ake and chain A, 4ake and chain A, cycles=0, object=aln

create rin, 1ake and aln, 1, 1

create rin, 4ake and aln, 1, 2

# morph from epymol

import rigimol rigimol.morph(“rin”, “rout”) 

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Notes:

1. Steps, length of movie and resolution are tunable. I just show the movies using default (above) script.

2. Once the rout is made, movie can be save easily using “file -> save movie as”

3. I used MacPyMOL to made the two movies.

Cartoon mode

Ball and stick mode

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