re amino acid atom names

 The amino acid atoms names are defined in the IUPAC-IUB
 pages and please note for pro-chiral atoms there is
 a difference between CD1 and CD2 as defined by the torsion
 angles see
 and pages ppep3.html /ppep1.html
 software like procheck's clean will check torsion angles
 prochirality rules also determine the names of some
 of the hydrogens see for example
 see the paper
 J. L. Markley, Y. Arata, A. Bax, C. W. Hilbers, R. Kaptein, B. D.
        Sykes, P. E. Wright, and K. Wuethrich,"Recommendations for the
        Presentation of NMR Structures of Proteins and Nucleic Acids,"
        Pure & Appl. Chem. 70, 117-142 (1998).
 link to pdf file on
 kim henrick
 Kim HENRICK    henrick { *at * } ::telephone:  +44 (0) 1223 494629