Dear all, 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.
Thanks a lot for your input, kind regards, Maria
