Editing Displaying Biochemical Properties (section)

== Bonds ==
PyMOL can deduce bonds from the PDB structure file, even if the '''CONECT''' records are missing.  In fact, PyMOL guesses bonding connectivity based on proximity, based on the empirical observation that two atoms of a given radius will not be generally closer than a certain distance unless they are bonded.

===Displaying double bonds===
<gallery widths="300px" heights="300px">
Image:DoubleBonds.png|Image showing double bonds in PyMOL.  Double bonds are supported in [[lines]] and [[sticks]].
</gallery>

You can go into the [[lines]] mode and turning on the valence display:
<source lang="python">
hide
as lines
set valence, 0.1
</source>

A higher value for valence spreads things out more. See the [[Valence]] page for more information on options for changing the appearance of the valence lines.

===Hydrogen bonds and Polar Contacts===

[[Image:Polar_contacts_small.png|thumb|Polar Contacts in PyMol|center|300px]]
Using the actions [A] button for an object or selection you can display Hydrogen bonds and Polar Contacts.
[A]->find->polar contacts-><select from menu>

The command behind the menus is the <b>dist</b>ance command called with the additional argument mode=2.

Parameters that control the the identification of H-bonds are defined as
 set h_bond_cutoff_center, 3.6
with ideal geometry and
 set h_bond_cutoff_edge, 3.2
with minimally acceptable geometry.

These settings can be changed *before* running the detection process (dist
command mode=2 or via the menus).

Note that the hydrogen bond geometric criteria used in PyMOL was designed to
emulate that used by [http://swift.cmbi.kun.nl/gv/dssp/ DSSP].

==== Hydrogen bonds between specific atoms ====
<source lang="python">
dist name, sele1, sele2, mode=2
</source>


==== Hydrogen bonds where find->polar contacts doesn't do what you need ====
You can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use [[h_add]] on the proteins, or provide ligands with valence information and then use h_add.

Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens.
<source lang="python">
# EXAMPLE 1: Show hydrogen bonds between protein 
# and docked ligands (which must have hydrogens)

load target.pdb,prot
load docked_ligs.sdf,lig

# add hydrogens to protein

h_add prot

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (lig and acc),(prot and don), 3.2
dist HBD, (lig and don),(prot and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD
</source>
<source lang="python">
# EXAMPLE 2
# Show hydrogen bonds between two proteins

load prot1.pdb
load prot2.pdb

h_add prot1
h_add prot2

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (prot1 and acc),(prot2 and don), 3.2
dist HBD, (prot1 and don),(prot2 and acc), 3.2
delete don
delete acc
hide (hydro)

hide labels,HBA
hide labels,HBD

# NOTE: that you could also use this approach between two
# non-overlapping selections within a single object.
</source>

The "polar contacts" mentioned above are probably better at finding hydrogen bonds than these scripts. "Polar contacts" check geometry as well as distance.

==== Details ====
Generally speaking, PyMOL does not have sufficient information to  rigorously determine hydrogen bonds, since typical PDB file are ambiguous with respect to charge states, bonds, bond valences, and tautomers. As it stands, all of those things are guessed heuristically. Rigorously determining the location of lone pair electrons and proton  coordinates from raw PDB files is a nontrival problem especially when arbitrary small molecule structures are present.  In addition, PyMOL would also need to consider the implied coordinate error due to overall structure resolution and local temperature factors before rigorously asserting than any specific hydrogen bond does or does not exist.

Furthermore, our hydrogen bond detection machinery was originally developed for purposes of mimicking Kabsch and Sander's DSSP secondary  structure assignment algorithm (Biopolymers 22, 2577, 1983) which is based on a rather generous notion of hydrogen bonding (see Kabsch Figure 1).

Although this approximate capability can be accessed via the distance command using mode=2, the criteria applied by our implementation may be based on heavy-atom coordinates (only) and does not necessarily correspond to anything rigorous or published.  So the bottom line is that PyMOL merely offers up putative polar contacts and leaves it to the user to determine whether or not the interactions present are in fact hydrogen bonds, salt bridges, polar interactions, or merely artifacts of incorrect assignments (i.e. two carbonyls hydrogen bonding because they're being treated like hydroxyls).

With respect to the h_bond_* settings, the angle in question for h_bond_cutoff_* and h_bond_max_angle is ADH, assuming H exists.  If H does not exist, then PyMOL will guess a hypothetical coordinate which may not actually be valid (in plane, etc.).  Tthe hydrogen must also lie within a cone of space with its origin on A (along B->A) and angular width h_bond_cone.  Since h_bond_cone in 180 by default, the present behavior is to simply reject any hydrogen bond where the hydrogen would lie behind the plane defined by the acceptor atom (A) in relation to its bonded atom(s) B (if any).  In other words, if B is only one atom (e.g.  C=O vs. C-O-C), then by default, HAB cannot be less then 90 degrees.

The two h_bond_power_* settings are merely fitting parameters which enable PyMOL to reproduce a curve shape reflecting Kabsch Figure 1.  The endpoints of the effective cutoff curve is a function of the two h_bond_cutoff_*  setting.