![]() In addition, PyMOL would also need to consider the implied coordinate error due to overall structure resolution and local temperature factors before rigorously asserting than any specific hydrogen bond does or does not exist.įurthermore, our hydrogen bond detection machinery was originally developed for purposes of mimicking Kabsch and Sander's DSSP secondary structure assignment algorithm (Biopolymers 22, 2577, 1983) which is based on a rather generous notion of hydrogen bonding (see Kabsch Figure 1).Īlthough this approximate capability can be accessed via the distance command using mode=2, the criteria applied by our implementation may be based on heavy-atom coordinates (only) and does not necessarily correspond to anything rigorous or published. Rigorously determining the location of lone pair electrons and proton coordinates from raw PDB files is a nontrival problem especially when arbitrary small molecule structures are present. As it stands, all of those things are guessed heuristically. Generally speaking, PyMOL does not have sufficient information to rigorously determine hydrogen bonds, since typical PDB file are ambiguous with respect to charge states, bonds, bond valences, and tautomers. "Polar contacts" check geometry as well as distance. The "polar contacts" mentioned above are probably better at finding hydrogen bonds than these scripts. 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. H., Nature, 229, 100 (1971).# EXAMPLE 2 # Show hydrogen bonds between two proteins load prot1. V., New Problems in the Physics of Glass (OTS Department of Commerce, District of Columbia, 1963). Kittel, C., Introduction to Solid State Physics (Wiley, New York, 1971). Quantitatively, these measurements also provide tests of theories of published vibrational models of homopolypeptides, and will give hydrogen bond strengths. The low temperature measurements presented here are the first made on a polypeptide in alpha and beta-conformation, and clearly show the one-dimensional nature of the α-helix and the two-dimensional nature of the β-sheet structure. The important lower-energy modes are well examined by specific heat measurements, which do not require single crystal samples, at low temperatures (for example, 1–20 K, where only the acoustic modes are excited thermally to any appreciable extent-1 K ∼0.7 cm −1). Basically, however, these latter methods examine the optical vibrational modes of a system, that is, those modes which are of energy higher than, for example, 70 cm −1. Recent advances in high polymer and solid state physics have enabled the vibrational aspects of the simpler homopolypeptides to be treated as normal-but complicated-polymers by the theoretical techniques of lattice dynamics based on the experimental methods of neutron, infrared and Raman spectroscopy. HOMOPOLYPEPTIDES provide good model systems for various aspects of proteins 1,2.
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