From: James S. <jms...@gm...> - 2012-06-28 07:50:28
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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 |
From: Thomas H. <sp...@us...> - 2012-06-30 20:38:17
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Hi James, retarding ordering of atoms, set this before loading the file: set retain_order, 1 See also: http://pymolwiki.org/index.php/Retain_order The atom names should actually not be changed, what did you do exactly? Cheers, Thomas James Starlight wrote, On 06/28/12 09:50: > 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 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |