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.


Blog at