Following question concerns Secondary Structure of hemoglobin pdb 1BZ0 If the PDB comes with HELIX information do I still need to add the secondary structure from the web (http://www.mbfys.lu.se/Services/SecStr/)?
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 I need to put in the web SS information, do I need to remove the pdb HELIX information from the file before putting in the HELIX info from the web? What do the numbers in the included HELIX info mean? Below are snips of both HELIX info, just so you can tell what I'm talking about. Included in 1BZ0.pdb: HELIX 1 1 PRO A 4 SER A 35 1 32 HELIX 2 2 PRO A 37 TYR A 42 5 6 HELIX 3 3 ALA A 53 ALA A 71 1 19 HELIX 4 4 MET A 76 ALA A 79 1 4 ... HELIX 29 29 LEU D 81 ASP D 94 1 14 HELIX 30 30 PRO D 100 GLU D 121 5 22 HELIX 31 31 PRO D 124 ALA D 142 1 19
