Changes in the default parameters¶
There are a lot of parameters that can be changed in the water bridge analysis, including the distances, angles, and the number of involved water molecules or residues.
atoms
: Atomic object from which atoms are considered
method
:'cluster'
or'chain'
, where ‘chain’ will find the shortest- water bridging path between two protein atoms
default is
'chain'
distDA
: maximal distance between water/protein donor and acceptor- default is
3.5
distWR
: maximal distance between considered water and any residue- default is
4
anglePDWA
: angle range where protein is donor and water is acceptor- default is
(100, 200)
anglePAWD
: angle range where protein is acceptor and water is donor- default is
(100, 140)
angleWW
: angle between water donor/acceptor- default is
(140, 180)
maxDepth
: maximum number of waters in chain/depth of residues in cluster- default is
2
maxNumRes
: maximum number of water+protein residues in cluster- default is
None
donors
: which atoms to count as donors- default is
['N', 'O', 'S', 'F']
acceptors
: which atoms to count as acceptors- default is
['N', 'O', 'S', 'F']
output
: return information arrays, (protein atoms, water atoms),- or just atom indices per bridge
Options are
'info'
,'atomic'
and'indices'
Default is'atomic'
isInfoLog
: whether to log information- default is
True
Here’s an example of how to apply changes in parameters:
In [1]: waterBridges_2 = calcWaterBridges(atoms, method='cluster', distWR=3.0, distDA=3.2, maxDepth=3)
@> 17 water bridges detected.
@> SER7 OG_21 A LYS110 NZ_838 A 4.70722699686344 1 ['A_1316']
@> GLY14 O_72 A SER47 O_328 A GLU50 N_347 A 5.288116583434976 4.544135231262378 5.10489901956934 1 ['A_1274']
@> PRO20 O_115 A GLU23 OE1_139 A 4.571172934816621 1 ['A_1292']
@> GLU23 OE2_140 A SER71 O_514 A HIS72 ND1_523 A 4.934310286149422 4.127239392136104 4.463734423103597 1 ['A_1244']
@> ASP42 OD2_301 A ARG40 NH2_286 A 5.163938516287738 1 ['A_1246']
@> ASP81 OD1_598 A THR84 OG1_621 A ARG40 NH2_286 A 4.415462942886057 4.365525627000715 3.9229717052255175 1 ['A_1262']
@> GLY14 O_72 A SER47 O_328 A GLU50 N_347 A 5.288116583434976 4.544135231262378 5.10489901956934 1 ['A_1274']
@> GLU50 OE2_355 A TYR131 OH_1009 A 5.157987010452818 1 ['A_1299']
@> ARG65 NH2_473 A ASP135 O_1037 A 4.820906553751068 1 ['A_1267']
@> GLU23 OE2_140 A SER71 O_514 A HIS72 ND1_523 A 4.934310286149422 4.127239392136104 4.463734423103597 1 ['A_1244']
@> GLN105 NE2_800 A LYS102 O_772 A LYS79 NZ_582 A 4.2363221076778395 3.8752885053889865 4.929221236666094 1 ['A_1249']
@> ASP81 OD1_598 A THR84 OG1_621 A ARG40 NH2_286 A 4.415462942886057 4.365525627000715 3.9229717052255175 1 ['A_1262']
@> GLN105 NE2_800 A LYS102 O_772 A LYS79 NZ_582 A 4.2363221076778395 3.8752885053889865 4.929221236666094 1 ['A_1249']
@> SER7 OG_21 A LYS110 NZ_838 A 4.70722699686344 1 ['A_1316']
@> LEU125 O_953 A GLY117 N_886 A 3.8595291163560352 1 ['A_1264']
@> GLU50 OE2_355 A TYR131 OH_1009 A 5.157987010452818 1 ['A_1299']
@> ARG65 NH2_473 A ASP135 O_1037 A 4.820906553751068 1 ['A_1267']