Nicolas Fusseder wrote: > When I run my make_chains.py script to generate a .chn file from a pdb > file I have been encountering an issue. It works perfectly for pdb files > where the chains are denoted as letters (A, B, C, D, ...) but pdb files > where numerics are used to denote chains (1, 2, 3, 4, ...) no .chn file > output. > > Below is the make_chains.py script I have been using: > > -------------------------------------------------- > env = environ() > mdl = model(env, file='c:/pdb/pdb1d3e.ent') > mdl.make_chains(file='1D3E', minimal_chain_length=30, minimal_resolution=4.0, > minimal_stdres=30, chop_nonstd_terminii=True, > structure_types='structureN structureX', > alignment_format='PIR') > > ---------------------------------------------------- > > for pdb id 1d3e (uses numerics): NO .CHN FILE OUTPUT > for pdb id 1e3l (uses letters): WORKS, 2 .chn files are output
It's not because the chains are numeric. The 1d3e structure was solved by Cryo-EM, and you've asked only for NMR or X-ray structures. Add 'structureE' to structure_types.
Ben Webb, Modeller Caretaker