Editing Dehydron (section)

== Usage ==
The plugin can be accessed using the following command:

<source lang="python">
wrappy [ selection [, angle_range [, max_distance [, desolv [, min_wrappers ]]]]]
</source>

[[Image:Dehydrons.png|580px|thumb|<b>Figure 0</b>: Dehydrons calculated and displayed in PyMOL.]]


Or using a graphical environment (see figure 0)


There are five parameters the user can change:

Two of them control the hydrogen bonds detection.

* Angle range: deviation in degrees from the optimal hydrogen bond angle (C=0 N-H).
* Max distance: maximum donor-acceptor distance in angstroms.

Although no thoroughly optimized, the default values for the hydrogen bonds parameters were adjusted to get a close agreement between the hydrogen bond listed by wrappy and the ones listed by the [http://swift.cmbi.ru.nl/servers/html/index.html What-If] server.

Another two control the dehydron detection.

* Desolvatation sphere radius: this parameter controls the radius of the two spheres centred at the Cα carbon of the donor and acceptor residues. A dehydron is defined by the number of "wrappers" inside this two spheres.<br>
* Min wrappers: a hydrogen bond surrounded with less "wrappers" than "min_wrappers" is a dehydron. Setting this parameter to a "high" value, something like 100, will return all main chain hydrogen bonds (according to the angle range and max distance parameters). The default value (19) was taken from a statistical analysis of ~7400 high-quality proteins form the Protein Data Bank (see below).
* Max wrappers: a hydrogen bond surrounded with more "wrappers" than "max_wrappers" is a buried hydrogen bond. The default value (35) was taken from a statistical analysis of ~7400 high-quality proteins form the Protein Data Bank (see below).

A wrapper is defined as a carbon atom not bonded directly to an oxygen or nitrogen atom, i.e. a non-polar carbon atom. The plug-in count as wrappers any non-polar carbon from any protein chain, organic ligand or other type of molecule, if the atoms belong "selection" (see below). This means that if you have, for example, a dimeric protein you will probably get different results for the dimer and for the isolated monomers. Instead, if you upload two (or more) different files the results will be independent because the plug-in does not count atoms from other objects

* Selection: This parameter allows the user to select which part of system is used to calculate dehydrons. This parameter is useful, for example, to calculate dehydronds for different objects independently or to easily calculate dehydrons with and without an organic ligand. The default selection is "all". Compute dehydrons for an specific selection is equivalent to delete all but the selected atoms and then compute dehydrons.