On 2/10/23 10:10 PM, Irawati Roy via modeller_usage wrote: > I am trying to build a model of a protein sequence where I have > structure of two domains of the protein as an input. One structure is > collected from PDB. another is simulation generated. I got the following > error: ... > _modeller.ModellerError: rdpdb___303E> No atoms were read from the > specified input PDB file, since the starting residue number and/or chain > id in MODEL_SEGMENT (or the alignment file header) was not found; > requested starting position: residue number " FIRST", chain " A"; atom > file name: A1.pdb > > The simulation generated structure file looks like following: > > ATOM 1 N MET X 1 43.720 45.860 63.480 0.00 0.00
You have asked Modeller to read residues from chain 'A', but your PDB file only has atoms in chain 'X'.
> for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): > mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:X'))
This will read atoms from each PDB file starting at the first residue in chain A and continuing until it reaches the last residue in chain X. This is probably not what you meant. Perhaps you meant something like the following instead:
for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): mdl = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain))
Ben Webb, Modeller Caretaker