negative sequence number start crashes spicker, at least in Concoord mode

[DanielRigden]

When pointing AMPLE to a directory of models to cluster (in this case from concoord, but I assume generally) Spicker crashes if the first residue number is -1 (or I assume anything negative). Renumbering to start from 1 runs fine.

I infer that this does not apply with the -homologs true flag on since the structure in question was acceptable in previous jobs based on multiple distant homologs.

Also worth noting for the record, that MSE residues and alternative conformations confuse Concoord. AMPLE should ideally have the option, at least via GUI2, to sort these things out for the user and run Concoord as part of a Concoord-mode job.