share/html/online/pdb.html

   1 <title>pdb file format</title>
   2 <body>
   3 <h1>pdb file format</h1>
   4 <h2>Description</h2>
   5
   6 Files with the <a href="pdb.html">.pdb</a> extension are molecular
   7 structure files in the protein databank file format.  The protein
   8 databank file format describes the positions of atoms in a molecular
   9 structure. Coordinates are read from the ATOM and HETATM records,
  10 until the file ends or an ENDMDL record is encountered.
  11 GROMACS programs can read and write a simlation box in the
  12 CRYST1 entry.
  13 The pdb format can also be used as a trajectory format:
  14 several structures, seperated by ENDMDL, can be read from
  15 or written to one file.
  16
  17 <p>
  18 <h2>Example</h2>
  19 An pdb file should look like this
  20 <PRE>
  21 ATOM      1  H1  LYS     1      14.260   6.590  34.480  1.00  0.00
  22 ATOM      2  H2  LYS     1      13.760   5.000  34.340  1.00  0.00
  23 ATOM      3  N   LYS     1      14.090   5.850  33.800  1.00  0.00
  24 ATOM      4  H3  LYS     1      14.920   5.560  33.270  1.00  0.00
  25 ...
  26 ...
  27 </PRE>
  28
  29 <p>
  30 <a href="../tutor/speptide/speptide.pdb.txt">speptide.pdb</a>:
  31 Protein structure file of Ribonuclease A speptide in protein data
  32 bank file format.
  33
  34 <p>
  35 Links to descriptions of the pdb format
  36 can be found on the <A HREF="../links.html">Links page</A>.
  37
  38 <p>
  39
  40 </body>