Hi,
I just noticed that Jmol 12.0.11 writes PDB files that don't match to the
specification.
for example: (col header for orientation)
1 2 3 4 5 6 7
8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETATM 1 S1 UNK 1 -7.220 -0.405 0.015 1.00 0.00
S
HETATM 2 H2 UNK 1 -8.120 0.570 0.003 1.00 0.00
H
HETATM 3 C3 UNK 1 -5.719 0.638 0.001 1.00 0.00
C
HETATM 4 H4 UNK 1 -5.731 1.260 -0.885 1.00 0.00
H
HETATM 5 H5 UNK 1 -5.730 1.283 0.870 1.00 0.00
H
HETATM 6 C6 UNK 1 -4.472 -0.244 0.011 1.00 0.00
C
HETATM 7 H7 UNK 1 -4.491 -0.903 -0.852 1.00 0.00
H
HETATM 8 H8 UNK 1 -4.490 -0.880 0.892 1.00 0.00
H
HETATM 9 C9 UNK 1 -3.183 0.582 -0.000 1.00 0.00
C
HETATM 10 H10 UNK 1 -3.173 1.223 -0.880 1.00 0.00
H
HETATM 11 H11 UNK 1 -3.172 1.246 0.862 1.00 0.00
H
One can see that the resName already starts in column 17 though in that
column one should find the altLoc with the
result that from column 17 everything is shifted 1 character to the left.
I have created the file by loading a GAMESS-US output file (in case that
makes any difference) and using the command:
write coords pdb "myFile.pdb" ;
Oliver
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