Shadow Contact Map
Basically, follow standard PDB formatting. Here is a sample pdb file, so you can see the format expected by the webtool.
Your pdb file MUST conform to the following standards.
Recognized residues include:
- No hidden characters. They can lead to unpredictable results. To avoid accidentally inserting them use a text editor such as vi, or emacs.
- If your file does not work with the page, only include lines that start with "ATOM" (to specify each atom), "TER" (to indicate a break between 2 chains) and "END" at the end of the file. Ligand atoms are also expected to be called ATOM, though they often appear as HETATMs in pdb files (leaving HETATM lines in your file will often lead to problems with the webtool).
- Chain identifiers are not used. If you have multiple chains, insert "TER" (left justified) between chains. The webtool will internally index the chains sequentially, starting with 1.
- Terminal oxygens (in proteins) are called, OXT and O (not O1 and O2).
- The file is not read past an "END" statement (ALL CAPS, left justified). If atoms appear after an END line, these atoms will not be included.
- Protein residues : All 20 amino acids (3 letter codes are used).
- RNA residues: CYT or C, GUA or G, URA or U and ADE or A.
- Modified RNA residue: MIA (2-methylthio-N6 isopentenyl adenosine).
- DNA residues: DG, DC, DA and DT.
- Ligands: SAM (S-Adenosylemethionine), GNP (Gpp(NH)p), ATP, ADP, AMP, FUA (Fusidic Acid), GTP, GDP and BMG (Bound MaGnesium ions).
- We are preparing a complete description on the precise parameterization of the ligands.
The shadow map is always based on atomic resolution contacts. There are three levels of output graining depending on the type of simulation you wish to run:
All-Atom Outputs all the atom-atom contacts. Format:
Chain i Atom i Chain j Atom j
All-Atom Calpha Considers a contact between two residues formed if any atom-atom contact is formed between the residues. Outputs the residue level contact map with the atom numbering of the Calpha atoms. Format:
Chain i Calpha_Atom i Chain j Calpha_Atom j
Calpha Considers a contact between two residues formed if any atom-atom contact is formed between the residues. Outputs the residue level contact map with residue numbering. Format:
Chain i Residue i Chain j Residue j
This page has been used to generate 1055 contact maps since 10/21/08.
Please direct questions and comments to firstname.lastname@example.org.
Page created and maintained by Jeff Noel and Paul Whitford