On 26-10-2006 10:24, [EMAIL PROTECTED] wrote: > I've been looking into sprouting hydrogens, and it's no problem. The only > thing is what do people really want. Please start discussing what you > want. > > 1) Only PDB models (like Chime)? > Not limited to PDB; any model that has 3D coordinates would be OK > 2) Only the 20 common amino acids (like Chime)? > All of the amino acids > 3) Just carbons or all atoms? > Carbons and amide nitrogens > 4) If not just PDB residues, suggestions for resolving oxidation state > ambiguities like -CCCO, which could be CH2CH2CH2OH or several other > possibilities. > This isn't a problem if only the amino acids are available since there isn't any ambiguity, true? > 5) If not just carbons, suggestions for resolving pKa issues. > If you stick with C and amide N then pKa won't be a problem. > 6) If not just carbons, suggestions for resolving dihedral selection. > see 5 > 7) full model or selected subsets? > no opinion
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