Editing Cluster mols (section)

== show_contacts ==
show_contacts is an expanded version of list_hbonds[http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/] that shows both favorable and unfavorable contacts between ligands and a protein receptor. show_contacts has been integrated into cluster_mols as a function and is executed automatically when clustering. It can also be run by itself, not in the context of cluster_mols. In the standalone case, the usage is as follows:

	show_contacts(selection,selection2,result="contacts",cutoff=3.6, bigcutoff = 4.0):

The arguments are as follows:
#selection -- pymol selection string for the protein
#selection2 -- pymol selection string for the ligands
#results -- prefix of the object that the distances should be shown in. (Default "contacts")
#cutoff -- Distance cutoff for what is considered an ideal hydrogen bond.
#bigcutoff -- Distance cutoff for a non-ideal hydrogen bond.


Output:
The output of show_contacts are a set of pymol distance objects. They are color-coded and size coded to indicate different interactions between the ligand and protein. They are controlled by the parameter indicated.

# thin-purple lines -- all possible polar contacts (acc-acc, don-don, acc-don) -- bigcutoff
# thick-yellow lines -- All ideal hydrogen bonds -- cutoff
# thin-yellow lines -- Non ideal hydrogen bonds -- bigcutoff
# thick-red lines -- Polar clashes, i.e. Donor-Donor, Acceptor-Acceptor -- cutoff