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.