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Hello Maria-- > I'm refining an RNA hairpin structure with xplor, using parameter file > nucleic.par. When uploading my final structures to the RCSB validation > server I notice that many angles and bond lengths do not cluster about > the mean values given in Clowney et al., JACS 1996, 118, 509-518, but > lie up to 2?/0.02A away from them. This is due to angles/bonds that are > defined by the same term in nucleic.par but do differ a little in > reality, e.g. Guanine C2-N3 should be 1.323A, Adenine C6-N1 should be > 1.351A and they are both set to 1.339A in nucleic par. > I do realize that all of these deviating values are well within the > 5?/0.05A limits but am just wondering if it is ok for the structures to > have all angles/bonds of one type shifted systematically by 2?/0.02A. I > noticed that I do not have this issue with cns, which defines every one > of these angles/bonds separately. Three bonds in three bases C2-N3 in GUA, C6-N1 in ADE and N3-C4 in CYT share the same value, and it seems that this bond length value dates from 1984, or earlier. I would welcome someone updating these values, but note that this will probably require that chemical types for those atoms be changed. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkvrAygACgkQPK2zrJwS/lYu8ACZAemserB6IFVdJLm+FRJmKwZ0 NZMAn37XWmot+FmMicqBn3ObJ/fFDi4v =CD0S -----END PGP SIGNATURE-----
