> They are different, especially at the ends of the helixes ... the web SS > seems to have longer helixes than the pdb HELIX info. Is one more > 'correct' than the other?
If in doubt, obtain DSSP (it might be installed locally already) and go with whatever it tells you: http://www.cmbi.kun.nl/gv/dssp/ Supposedly the PDB uses this to determine the HELIX and SHEET records - which doesn't mean they didn't screw up, but DSSP is pretty standard. You can either replace the records in the PDB file (time-consuming, but several people have written scripts to do this, myself included), or enter the commands to assign structure manually in pymol, e.g. alter <selection>, ss='H' -Nat
