Scripts: selLys.py

import chimera
from chimera import specifier, selection
from StructMeasure.DistMonitor import addDistance
sel = selection.ItemizedSelection()
sel.merge(selection.REPLACE, specifier.evalSpec(":LYS@NZ"))
nearRes = []
sel2 = selection.ItemizedSelection()
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
dists = set()
for a in sel.atoms():
        sel2.clear()
        sel2.add(a)
        sel2.merge(selection.REPLACE, specifier.zone(sel2, specifier.ATOM, None, 8.0, models))
        nearNZ = [sa for sa in sel2.atoms() if sa.name == "NZ" and sa.residue.type == "LYS"]
        nearNZ.remove(a)
        for nz in nearNZ:
                if (a, nz) in dists: continue
                addDistance(a, nz)
                dists.add((nz,a))
        selRes = [nz.residue for nz in nearNZ]
        nearRes.extend(selRes)
selection.setCurrent(nearRes)