PDB CRYST1 not loaded correctly (?) #876
Description
I'm having an issue where pytraj is not loading the PBC information from PDB files. For example, with the following file (I just took the head from a larger file, but the same thing applies to the larger files)
$ cat example.pdb
CRYST1 51.263 51.263 51.263 90.00 90.00 90.00 P 1 1
ATOM 1 N ARG A 1 4.481 11.293 0.204 0.00 0.00 C1 N
ATOM 2 CA ARG A 1 5.137 10.135 0.877 0.00 0.00 C1 C
ATOM 3 C ARG A 1 5.356 9.056 -0.221 0.00 0.00 C1 C
ATOM 4 O ARG A 1 4.487 8.823 -1.054 0.00 0.00 C1 O
ATOM 5 CB ARG A 1 4.154 9.632 2.008 0.00 0.00 C1 C
ATOM 6 CG ARG A 1 4.819 8.703 2.982 0.00 0.00 C1 C
ATOM 7 CD ARG A 1 6.020 9.239 3.802 0.00 0.00 C1 C
ATOM 8 NE ARG A 1 5.551 10.357 4.670 0.00 0.00 C1 N
ATOM 9 CZ ARG A 1 6.185 10.965 5.621 0.00 0.00 C1 C
pytraj does not detect PBCs
$ python -c 'import pytraj as pt; print(pt.load("example.pdb"))'
<pytraj.Trajectory, 1 frames, include:
<Topology: 9 atoms, 1 residues, 1 mols, non-PBC>>
I checked both gmx check, vmd, and mdtraj for this file, and they do load the box coordinates.