On 11/17/2010 11:07 AM, Irene Newhouse wrote: > I'm trying to get the format right for a multiple alignment I did with > a Clustal W server to use as input to modeller. I don't understand the > error message ... > _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 " A", chain " 3"; atom file name: > /home/newhoir/rubber/atom_files/2d2r.pdb
You have asked Modeller to read structural information from a PDB file, starting at residue number "A" in chain "3". Modeller's simply telling you it can't find that residue and chain. Most likely you actually meant residue "3" in chain "A" - i.e. you simply have the residue numbers and chain IDs the wrong way round in your alignment files.
Ben Webb, Modeller Caretaker