Thanks Miguel and Angel!
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
--
* Toni Hermoso Pulido
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