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Regarding H-bonds. There isn't a built-in function yet, but you can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use h_add on the proteins or provide ligands with valence information and then use h_add.
Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens.
# EXAMPLE 1: Show hydrogen bonds between protein
# and docked ligands (which must have hydrogens)
load target.pdb,prot
load docked_ligs.sdf,lig
# add hydrogens to protein
h_add prot
select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (lig and acc),(prot and don), 3.2
dist HBD, (lig and don),(prot and acc), 3.2
delete don
delete acc
hide (hydro)
hide labels,HBA
hide labels,HBD
# EXAMPLE 2: Show hydrogen bonds between two proteins
load prot1.pdb
load prot2.pdb
h_add prot1
h_add prot2
select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (prot1 and acc),(prot2 and don), 3.2
dist HBD, (prot1 and don),(prot2 and acc), 3.2
delete don
delete acc
hide (hydro)
hide labels,HBA
hide labels,HBD
# NOTE: that you could also use this approach between two
# non-overlapping selections within a single object.
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发表于 2011-10-7 06:39:00