Shadow Contact Map
(beta version)

Thank you for using the Onuchic Group`s structure-based potential software. This module will take your pdb and produce an atomic resolution contact map. When using the Shadow contact map, reference Noel and Onuchic (in preparation). For an description of the algorithm click here.

Upload PBD file  help, example pdb

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NOTES ON USING THIS SOFTWARE

PDB file

Only lines that start with "ATOM" will be recognized for processing.
Chain identifiers are not used. To indicate the end of a chain, use "TER" lines (left justified) between chains.
The file is read until an "END" statement (left justified) is encountered.

Recognized residues:

  • Protein residues : All 20 amino acids.
  • RNA residues: CYT or C, GUA or G, URA or U and ADE or A.
  • DNA residues: DG, DC, DA, DT.
  • Ligands: SAM (S-Adenosylemethionine), GNP (Gpp(NH)p)

Graining

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 96 contact maps since 10/24/08.
Page created and maintained by Jeff Noel and Paul Whitford