Hello,
I have found the following problem and would like to ask for your help. If I run pdbfixer on the structure 4rpy pdbfixer 4rpy.pdb, two overlapping residues remain in output.pdb:
These are the two residues in output.pdb:
HETATM 6291 H11 PPV A 413 5.218 1.927 15.522 1.00 0.00 H
HETATM 6292 P1 PPV A 413 3.039 1.897 15.348 1.00 0.00 P
HETATM 6293 O21 PPV A 413 1.693 2.415 15.807 1.00 0.00 O
HETATM 6294 H21 PPV A 413 1.095 1.399 15.555 1.00 0.00 H
HETATM 6295 O31 PPV A 413 3.147 1.663 13.861 1.00 0.00 O
HETATM 6296 OPP PPV A 413 3.131 0.432 16.015 1.00 0.00 O
HETATM 6297 P2 PPV A 413 2.817 0.284 17.591 1.00 0.00 P
HETATM 6298 O12 PPV A 413 2.075 1.589 17.929 1.00 0.00 O
HETATM 6299 H12 PPV A 413 1.502 1.355 18.950 1.00 0.00 H
HETATM 6300 O22 PPV A 413 1.999 -0.974 17.716 1.00 0.00 O
HETATM 6301 O32 PPV A 413 4.191 0.162 18.208 1.00 0.00 O
HETATM 6302 H32 PPV A 413 4.609 -1.001 18.180 1.00 0.00 H
HETATM 6303 N1 DCP A 414 6.193 6.914 11.967 1.00 0.00 N
HETATM 6304 C2 DCP A 414 7.088 7.176 10.919 1.00 0.00 C
HETATM 6305 N3 DCP A 414 8.427 7.125 11.124 1.00 0.00 N
HETATM 6306 C4 DCP A 414 8.914 6.803 12.339 1.00 0.00 C
HETATM 6307 C5 DCP A 414 8.041 6.537 13.387 1.00 0.00 C
HETATM 6308 H5 DCP A 414 8.545 7.026 14.438 1.00 0.00 H
HETATM 6309 C6 DCP A 414 6.668 6.588 13.174 1.00 0.00 C
HETATM 6310 H6 DCP A 414 6.377 7.152 14.261 1.00 0.00 H
HETATM 6311 O2 DCP A 414 6.641 7.473 9.792 1.00 0.00 O
HETATM 6312 N4 DCP A 414 10.261 6.745 12.528 1.00 0.00 N
HETATM 6313 HN41 DCP A 414 11.347 6.491 11.988 1.00 0.00 H
HETATM 6314 HN42 DCP A 414 10.449 5.563 12.860 1.00 0.00 H
HETATM 6315 C1' DCP A 414 4.750 6.958 11.685 1.00 0.00 C
HETATM 6316 H1' DCP A 414 4.876 8.257 11.721 1.00 0.00 H
HETATM 6317 C2' DCP A 414 4.363 5.557 11.208 1.00 0.00 C
HETATM 6318 H2'1 DCP A 414 4.558 4.367 10.741 1.00 0.00 H
HETATM 6319 H2'2 DCP A 414 5.527 5.083 11.304 1.00 0.00 H
HETATM 6320 C3' DCP A 414 3.802 4.933 12.471 1.00 0.00 C
HETATM 6321 H3' DCP A 414 4.768 4.242 12.880 1.00 0.00 H
HETATM 6322 C4' DCP A 414 3.058 6.121 13.056 1.00 0.00 C
HETATM 6323 H4' DCP A 414 1.830 5.800 12.891 1.00 0.00 H
HETATM 6324 O4' DCP A 414 3.961 7.215 12.845 1.00 0.00 O
HETATM 6325 O3' DCP A 414 2.970 3.791 12.251 1.00 0.00 O
HETATM 6326 HO3' DCP A 414 3.342 2.647 12.006 1.00 0.00 H
HETATM 6327 C5' DCP A 414 2.713 5.933 14.528 1.00 0.00 C
HETATM 6328 H5'1 DCP A 414 2.370 4.860 14.958 1.00 0.00 H
HETATM 6329 H5'2 DCP A 414 1.462 5.930 14.770 1.00 0.00 H
HETATM 6330 O5' DCP A 414 3.970 5.770 15.169 1.00 0.00 O
HETATM 6331 PA DCP A 414 4.141 4.884 16.484 1.00 0.00 P
HETATM 6332 O1A DCP A 414 5.535 5.275 16.906 1.00 0.00 O
HETATM 6333 O2A DCP A 414 2.963 5.176 17.431 1.00 0.00 O
HETATM 6334 HOA2 DCP A 414 3.174 4.832 18.589 1.00 0.00 H
HETATM 6335 O3A DCP A 414 4.199 3.393 15.882 1.00 0.00 O
HETATM 6336 PB DCP A 414 3.040 2.383 15.381 1.00 0.00 P
HETATM 6337 O1B DCP A 414 3.332 2.026 13.945 1.00 0.00 O
HETATM 6338 O2B DCP A 414 1.660 2.855 15.739 1.00 0.00 O
HETATM 6339 HOB2 DCP A 414 0.832 3.711 15.637 1.00 0.00 H
HETATM 6340 O3B DCP A 414 3.427 1.075 16.256 1.00 0.00 O
HETATM 6341 PG DCP A 414 3.352 0.979 17.874 1.00 0.00 P
HETATM 6342 O1G DCP A 414 2.278 -0.068 18.120 1.00 0.00 O
HETATM 6343 O2G DCP A 414 4.739 0.522 18.258 1.00 0.00 O
HETATM 6344 HOG2 DCP A 414 5.196 1.316 19.010 1.00 0.00 H
HETATM 6345 O3G DCP A 414 2.985 2.364 18.345 1.00 0.00 O
HETATM 6346 HOG3 DCP A 414 3.258 2.728 19.441 1.00 0.00 H
I would also like to ask how PDBFixer selects from alternative positions? Do I understand correctly from source code that if there are multiple alternative positions for an atom, PDBFixer takes position A?
Hello,
I have found the following problem and would like to ask for your help. If I run pdbfixer on the structure 4rpy
pdbfixer 4rpy.pdb, two overlapping residues remain in output.pdb:These are the two residues in output.pdb:
I would also like to ask how PDBFixer selects from alternative positions? Do I understand correctly from source code that if there are multiple alternative positions for an atom, PDBFixer takes position A?