Follow-up Comment #4, sr #2998 (project relax):
The problem is that the PDB file 1RTE is corrupt (specifically in the CONECT
records which point to non-existent atoms), and relax's PDB reader cannot
currently handle such corruptions. One fix is to delete all CONECT records in
the PDB file. The other is to use the ScientificPython parser instead of the
internal relax parser.
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