VMD-L Mailing List

From: Nuno R. L. Ferreira (nunolf_at_ci.uc.pt)
Date: Tue Feb 14 2006 - 04:42:50 CST

Hi Teresa

You could write that information as REMARK, or better, use the HELIX, SHEET ... tags for the secondary structure. From the top of my head, I do not know the format of this tags inside the PDB, but you can check it in the PDB site.

# select one atom of each residue
set sel [atomselect top "protein and name CA"]
# create a list of secondary structure (stride)
# C = coil ; T = turn
# E = beta sheet ...; check stride
sel struct_list [$sel get structure]

You then must determine which residues are in beta-sheet, which are in helix conformation ...

With this list, you can then do a parser, taking in consideration the format of the tags that I just mentioned, and
output a formated text to be the new header of your pdb.

Best,
Nuno

  ----- Original Message -----
  From: Palmer, Teresa
  To: vmd-l_at_ks.uiuc.edu
  Sent: Monday, February 13, 2006 10:57 PM
  Subject: vmd-l: Writing a pdb file with header information

  Hi,

  I have a file which just consists of a list of all the atoms and the co-orinate information etc. I can load it into VMD and view the secondary structure elements. I'd really like to output the different secondary structure elements in a form similar to a pdb header - i.e. get all the information as to the alpha helices and beta sheets. Is there any way I can do this using VMD?

  Thanks

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