Hi, i read a PDB file with PDBFileReader.getStructure and want to extract the backbone of a chain with StructureTools. Now i have seen that for entries e.g.
ATOM 3505 N GLN A 27 32.144 27.054 0.696 1.00 47.70 N ATOM 3506 CA GLN A 27 32.507 26.162 -0.401 1.00 42.73 C ATOM 3507 C GLN A 27 31.388 26.137 -1.437 1.00 40.44 C ATOM 3508 O GLN A 27 30.205 26.248 -1.096 1.00 41.47 O ATOM 3509 CB GLN A 27 32.729 24.738 0.121 1.00 42.51 C ATOM 3510 CG GLN A 27 34.124 24.449 0.611 1.00 39.02 C ATOM 3511 CD GLN A 27 34.158 23.301 1.593 1.00 41.90 C ATOM 3512 OE1 GLN A 27 33.982 22.143 1.214 1.00 39.58 O ATOM 3513 NE2 GLN A 27 34.386 23.615 2.869 1.00 43.85 N ATOM 3514 N SER A1027 31.762 25.988 -2.703 1.00 33.42 N ATOM 3515 CA SER A1027 30.776 25.929 -3.769 1.00 31.11 C ATOM 3516 C SER A1027 29.915 24.723 -3.462 1.00 27.99 C ATOM 3517 O SER A1027 30.418 23.706 -2.991 1.00 29.25 O ATOM 3518 CB SER A1027 31.449 25.746 -5.130 1.00 22.71 C ATOM 3519 OG SER A1027 30.542 25.185 -6.056 1.00 28.95 O ATOM 3520 N LEU A2027 28.619 24.838 -3.718 1.00 25.68 N ATOM 3521 CA LEU A2027 27.714 23.743 -3.444 1.00 23.42 C ATOM 3522 C LEU A2027 27.489 22.933 -4.694 1.00 24.27 C ATOM 3523 O LEU A2027 26.750 21.950 -4.675 1.00 28.95 O ATOM 3524 CB LEU A2027 26.391 24.278 -2.906 1.00 23.54 C ATOM 3525 CG LEU A2027 26.547 25.090 -1.619 1.00 22.93 C ATOM 3526 CD1 LEU A2027 25.179 25.430 -1.056 1.00 26.74 C ATOM 3527 CD2 LEU A2027 27.361 24.285 -0.603 1.00 19.54 C the two residues SER and LEU are not counted. However, the fasta file from pdb.org website shows both residues for that chain. I wonder how the two entries A1027 and A2027 are interpreted by StructureTools. Thanks for any hints Martin _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
