On 11/03/2010 02:57 PM, Ann Spevacek wrote: > I am trying to align two models, one an NMR structure (1XYX.pdb) and > one a simulation (frame100.pdb) and I get the following error: > > 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: ./frame100.pdb
OK, so you have asked Modeller to read coordinates from the "frame100.pdb" PDB file, starting at the first residue in the A chain.
> This is what the frame100.pdb file looks like:
There is no "A" chain in this PDB file... so how will Modeller be able to read it?
> And this is the salign.py file that I am trying to use: > > # Illustrates the SALIGN multiple structure/sequence alignment > > from modeller import * > > log.verbose() > env = environ() > env.io.atom_files_directory = './:../atom_files/' > > aln = alignment(env) > for (code, chain) in (('1XYX', 'A'), ('frame100', 'A')):
Replace the second 'A' with '', to read from a chain with no ID, as in your PDB file.
Ben Webb, Modeller Caretaker