Hi Yang Li: Macromolecular crystal refinement programs use ideal bond lengths and angles.
The simplest ones just assume any carbon-carbon single bond (C-C) is the same as any other, and use one average value, and any carbon-carbon double bond (C=C) is the same as any other, and use another average value, and so on for all possible linkages. Better ones treat individual cases differently, so that the Calpha-Cbeta bond in amino acids is compared only to other Calpha-Cbeta bond lengths, for example. The best ones will have a specific average value for each Calpha-Cbeta bond length for each amino acid that has this bond. Similarly for angles. The standard value is usually established from very high resolution crystal structures of (for example) individual amino acids, and/or quantum chemistry calculations. Various different methods are employed to penalize deviation from ideality in a refinement. It is common to use a simple quadratic penalty, which can be characterized by a Hook's Law spring constant, and this is justified where the harmonic approximation for bond potentials is valid (and it should be in crystal structures). Each refinement program has its own way of implementing the above, so the best thing to do is to look at the bond parameter dictionaries that your program uses. I hope that comes closer to answering your question. All the best, Bill Scott yang li wrote: > By the way, I think my bad english embarrassed my meaning. What I want > to say > is which bond length is used as the standard? the C=N or Ca-N or even the > side chains? > Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or > others. > At first I suppose the bond length only calculate the C=N bond, and > donnot know which one > is used as the aggel. It should be a quite stupid question for whom knows > it. Just forget it. >
