[modeller_usage] Selection criteria for building sequence database - pdball.pir

Hi,

I'm trying to rebuild the pdball.pir file from a set of pdb files, using the model.make_chain() as mentioned in modeller website and I noticed certain filter criteria as parameters to make_chain() such as

minimal_chain_length=30 minimal_stdres=30 chop_nonstd_terminii=True max_nonstdres=10 minimal_resolution=99.0 structure_types='structureN structureX'

And while processing I found that certain pdb files are skipped due to this filter criteria. My query is 1) Are these the standard criteria for building pir file? 2) Or adjusting the values to 0 (except min. res) will alter the purpose ?

Thanks for any help

Praveen Raj