Dear Pymol Users!


I've forced with the problem of missing correct atom numbering order during processing of my pbd structure.


E.g I had a mollecule of caffein where each atoms had its own number ( e.g N1 or N3 etc)

HETATM 2252  N1  CFF A 330       9.174 -33.156 -31.881  1.00147.73           N 
HETATM 2253  C2  CFF A 330       9.511 -33.973 -32.948  1.00148.15           C 
HETATM 2254  C10 CFF A 330      10.180 -32.790 -30.862  1.00138.32           C 
HETATM 2255  C6  CFF A 330       7.880 -32.698 -31.748  1.00147.40           C 
HETATM 2256  N3  CFF A 330       8.560 -34.329 -33.882  1.00149.30           N 
HETATM 2257  O11 CFF A 330      10.781 -34.432 -33.079  1.00142.40           O 
HETATM 2258  C12 CFF A 330       8.923 -35.204 -35.004  1.00147.42           C 
HETATM 2259  C4  CFF A 330       7.287 -33.864 -33.735  1.00146.85           C 
HETATM 2260  C5  CFF A 330       6.925 -33.068 -32.699  1.00145.81           C 
HETATM 2261  N9  CFF A 330       6.240 -34.112 -34.550  1.00147.23           N 
HETATM 2262  O13 CFF A 330       7.552 -31.908 -30.705  1.00147.52           O 
HETATM 2263  N7  CFF A 330       5.617 -32.775 -32.828  1.00147.22           N 
HETATM 2264  C8  CFF A 330       5.235 -33.422 -33.954  1.00148.06           C 
HETATM 2265  C14 CFF A 330       4.727 -31.975 -31.994  1.00145.92           C 

as the consequence I've obtained pdb of this molecule with changing atom order and (that is expesiaaly crusial ) missing atom names

ATOM   3076  N   CFF A 309      34.653  29.507  62.240  1.00  0.00           N 
ATOM   3077  N   CFF A 309      34.101  31.995  64.970  1.00  0.00           N 
ATOM   3078  N   CFF A 309      34.561  30.167  66.245  1.00  0.00           N 
ATOM   3079  N   CFF A 309      34.804  28.565  64.396  1.00  0.00           N 
ATOM   3080  C   CFF A 309      34.394  30.795  62.724  1.00  0.00           C 
ATOM   3081  C   CFF A 309      34.844  28.368  63.031  1.00  0.00           C 
ATOM   3082  C   CFF A 309      34.674  29.255  60.791  1.00  0.00           C 
ATOM   3083  C   CFF A 309      34.304  30.906  64.146  1.00  0.00           C 
ATOM   3084  C   CFF A 309      33.873  33.404  64.619  1.00  0.00           C 
ATOM   3085  C   CFF A 309      34.302  31.471  66.198  1.00  0.00           C 
ATOM   3086  C   CFF A 309      34.489  29.789  64.952  1.00  0.00           C 
ATOM   3087  C   CFF A 309      34.554  27.304  65.108  1.00  0.00           C 
ATOM   3088  O   CFF A 309      33.999  31.682  61.969  1.00  0.00           O 
ATOM   3089  O   CFF A 309      35.172  27.317  62.481  1.00  0.00           O 
ATOM   3090  H   CFF A 309      34.383  32.108  67.079  1.00  0.00           H 

in the second example you can see that all Nitrogens are just N without numbers etc.

1- Does it possible to resutn to the second pdb file initial correct atom numbering ?
2- How I could prevent in future deleating of such numbers ? (It's occured after I add missing Hydrogens and connect enties to my mollecule by PYMOL)


Thanks for help,

James