I located two methods for assessing number of H-bonds between a receptor &
dock ligand. The first method results in the usual dashed yellow lines for
objects HBA and HBD, depending on what was found.
The second method (bottom) shows the # H-bonds if a distance is greater than
a radius. However, these methods (obviously differ). For a given ligand
the first shows 2 bonds and the second lists only one (and it's not the 3.2
setting, since raising that to 3.5 didn't make them the same).
The dilemma is that I either need to fetch the total count from the first
method, or draw the bonds that are identified by the second, since the first
method only draws objects and the second only enumerates.
cmd.bg_color("white")
cmd.h_add("prot")
cmd.select("don","(elem n,o and (neighbor hydro))")
cmd.select("acc","(elem o or (elem n and not (neighbor hydro)))")
cmd.dist("HBA","(lig and acc)","(prot and don)","3.2")
cmd.dist("HBD","(lig and don)","(prot and acc)","3.2")
cmd.delete("don")
cmd.delete("acc")
cmd.hide("(hydro)")
cmd.hide("labels","HBA")
cmd.hide("labels","HBD")
cmd.show("surface","prot")
sele1 = "lig & (donors | acceptors)"
sele2 = "prot & (donors | acceptors)"
radius = 3.5
D = cmd.find_pairs(sele1, sele2, mode = 1, cutoff = radius)
print("number of h-bonds: ", len(D))
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