Hello,
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
Thank you for your help,
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
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Modeller Caretaker -
Nicolas Fusseder