Test input files compatibility
We recommend on performing the simple following test to see that your input file sequences obey PROSS formats.
example is given on PDB entry 1AHW chain B:
- Extract the sequence from the PDB file (command line example for PyMOL: save 1AHW_B.fasta, 1AHW and chain B).
- Align the sequence from the sequence file and the PDB-extracted sequence. The sequence from the sequence file should be equal or longer than the PDB sequence, that gaps in the alignment (if exist) are seen only in the PDB-extracted sequence and that no point mutations are seen (easy alignment: BLAST2SEQ).
If preparing the file on a PC, open the file in a Unix based system (Mac for instance) and make sure that there are no unexpected hidden characters.