> Hello, > > I am working with PDB consensus coordinates derived from several > structures and I'm not able to view the molecule as backbone, wireframe, > etc. in Jmol. I only get atoms as unconnected spots. I have no problem > with Rasmol or Chime. > Any idea? I send a PDB test file.
Your file format is incorrect. In the case of N, C, and O atoms you have put the element symbol in the column reserved for the the alphabetic remoteness indicator and have left the element symbol blank. You have: ATOM 1 N GLY 1 4.794 -0.966 -4.193 1.00 99.00 ATOM 2 CA GLY 1 3.792 0.001 -4.433 1.00 99.00 ATOM 3 C GLY 1 2.880 0.006 -3.283 1.00 99.00 ATOM 4 O GLY 1 2.357 -1.002 -2.940 1.00 99.00 You need: ATOM 1 N GLY 1 4.794 -0.966 -4.193 1.00 99.00 ATOM 2 CA GLY 1 3.792 0.001 -4.433 1.00 99.00 ATOM 3 C GLY 1 2.880 0.006 -3.283 1.00 99.00 ATOM 4 O GLY 1 2.357 -1.002 -2.940 1.00 99.00 I have attached 'repaired.pdb' In addition, filling in columns 77 & 78 with the element symobl is recommended. An excerpt from the PDB specification is below. Miguel * Six characters (columns) are reserved for atom names, assigned as follows. COLUMN VALUE ----------------------------------------------------------------------- 13 - 14 Chemical symbol - right justified, except for hydrogen atoms 15 Remoteness indicator (alphabetic) 16 Branch designator (numeric) 77 - 78 Element symbol, right-justified
repaired.pdb
Description: Protein Databank data
