Python Programming for Biology: Bioinformatics and Beyond

16

It would also be possible to find a new medioid (closest to mean) structure and use that

for the RMSD calculation.

17

In a PDB file the codes in the strictest sense will have three characters, i.e. ‘A ‘ or ‘G ‘,

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but our reader function removes the excess spaces.

18

The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC.

19

Note that during testing of this code on some Linux computer platforms, we discovered

that in order for the PyMol program to work properly from a Python script we also had to

define the ‘PYMOL_PATH’ environment variable, which can be done from within Python

by  importing  the  os  module  and  then  setting  os.environ[‘PYMOL_PATH’]  =

os.path.dirname(pymol.__file__):  the  location  where  PyMol’s  Python  modules  are

installed.

20

This protein is found in the membranes of red blood cells.

21

i.e. the hydrophobic helices that anchor this protein in a lipid membrane.

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