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
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