Crystallography‎ > ‎Molecular graphics‎ > ‎Pymol‎ > ‎

Displaying biochemical properties

Showing Residues with functional groups 

(Example 2JG4)

remove resn hoh # remove water 
h_add # add hydrogens 
as surface
color grey90 
color slate, resn lys # lysines in light blue
color paleyellow, resn cys # cysteines in light yellow 
color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red
IMPORTANT: When using surface representation, PyMol shows the Connolly surface (the surface that would be traced out by the _surfaces_ of waters in contact with the protein at all possible positions). Therefore, hydrogens should be added (and water removed) in order to get the most biophysically relevant representation.

Show hydrophobic residues

select hydrophobic,(resn ala+gly+val+ile+leu+phe+met)*
show surface
color orange, hydrophobes

*And we can argue on the selection of Hydrophobic residues here. I would go with this:

So to be more precise:

select VERY-hydrophobic,(resn val+ile+leu+met+phe+trp+cys)
show surface
color orange, VERY-hydrophobic

select LESS-hydrophobic,(resn ala+tyr+his+thr+ser+pro+gly)
show surface
color yelloworange, LESS-hydrophobic

select PARTIALLY-hydrophobic,(resn arg+lys)
show surface
color lightblue, PARTIALLY-hydrophobic

Hydrogen bonds between specific atoms or objects

dist name, sele1, sele2, mode=2