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· Distances Bridges

Distance calculation between two known forms of a macromolecule

Input
You need to input two pdb files and the range of distances you want to examine.

Output
A table of distances that fall within the specified range.

Job title: (Only alphanumerical characters)


PDB file for the first form (e.g. open form)
(Ex: open_ca.pdb)



PDB file for the second form (e.g. resting form)
(Ex: closed_ca.pdb)



Distance
Tolerance


Input data formats

  • The job title is just for your own identification. Please note that it will show up in the public job queue (but your results will not be public).

  • The coordinate file should be in PDB format, with only a single structure (no multiple models). Atoms marked with alternate residue flags will be removed. Whatever atoms (ATOM card) are in the file will be used for the calculation (but not the HETATM ones).

  • This code is specific for multimers. It knows how to handle these. It will not consider Glycine positions as likely positions for attaching a Cysteine. For the moment, the reported distances refer to distance between C-alpha atoms...



  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 12:45 December 14, 2015.