When using the Mutagenesis wizzard to do point mutations on proteins, the AtomName column of the PDB file, specially with hydrogens, is being written in the wrong order. Some other molecular viewers can't build the bonds properly when reading the exported PDB file.
PyMol exported hydrogens (ie. after mutating residue 24 to PHE)
ATOM 326 2HB PHE 24 -4.858 -11.465 -6.291 1.00 0.00 H
ATOM 327 3HB PHE 24 -5.548 -10.850 -7.766 1.00 0.00 H
ATOM 328 1HD PHE 24 -5.933 -8.520 -8.040 1.00 0.00 H
ATOM 329 2HD PHE 24 -3.274 -9.813 -4.921 1.00 0.00 H
ATOM 330 1HE PHE 24 -5.801 -6.215 -7.196 1.00 0.00 H
ATOM 331 2HE PHE 24 -3.158 -7.501 -4.072 1.00 0.00 H
This is how the format should look like.
ATOM 326 HB2 PHE 24 -4.858 -11.465 -6.291 1.00 0.00 H
ATOM 327 HB3 PHE 24 -5.548 -10.850 -7.766 1.00 0.00 H
ATOM 328 HD1 PHE 24 -5.933 -8.520 -8.040 1.00 0.00 H
ATOM 329 HD2 PHE 24 -3.274 -9.813 -4.921 1.00 0.00 H
ATOM 330 HE1 PHE 24 -5.801 -6.215 -7.196 1.00 0.00 H
ATOM 331 HE2 PHE 24 -3.158 -7.501 -4.072 1.00 0.00 H
Dear Schrodinger,
When using the Mutagenesis wizzard to do point mutations on proteins, the AtomName column of the PDB file, specially with hydrogens, is being written in the wrong order. Some other molecular viewers can't build the bonds properly when reading the exported PDB file.
PyMol exported hydrogens (ie. after mutating residue 24 to PHE)
This is how the format should look like.
Best regards Pedro