My software notes

April 6, 2013

[PyMOL] compute molecular weight

Filed under: pymol/ molmol — kpwu @ 3:06 am

From PyMOL 1.5, there is a quick way to compute the object molecular weight.

Simple click “A” right next to the (select) object, and go down to “compute”, then choose “molecular weight” to calculate MW of object either “explicit” or “with missing hydrogens” mode. The missing hydrogens mode means PyMOL automatically add missed protons of object and calculate the proton-added MW.

I found that object with water oxygens (commonly in crystal structures) will also be included while running this command. Users may need to be careful about it.

Note: The calculated MW is actually a bit different from values (same sequences, of course!) I used “protein calculator” or “ExPASy get pI/Mw“. The value from PyMOL are not average/monoisotopic MW as calculated from both two sites (both two sites gave me exact same numbers). I actually don’t know why..

Here is the snapshot. The computed MW can be seen in the pymol terminal (boxed). Top number includes missing hydrogens.


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”) 


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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