· Delarue web servers
· Nomad Flow-chart
· Normal Mode calculation
  · Examples (Movies)
  · Submit a job (from PDB file)
  · Split trajectory (for MR)
  · Generate decoys (MixMod)
  · Elastic Energy (Perturb. Anal.)
· Overlap coefficients
  · Include Profit step
  · Without Profit!
· X-Ray refinement
  · Standard refinement
  · Screening Mol. Repl. Solns.
· EM refinement
  · Documents/Examples
  · Get Structure Factors
  · Submit a job (no NCS)
  · Submit job with NCS
· Docking refinement
  · Submit a job (refinement)
  · Submit a job (scanning)
· Force field methods
  · Energy minimization
  · Gromacs NMA
· References
· Homes/Links
· Job queue status

Split trajectory into pieces

This is a facility to convert the result of "Submit a job" option into a series of individual PDB files for Molecular Replacement (MR) applications. There will be 30 PDB files, tarred in a single file. Only the first 15 are really independent (with increasing amplitude) as the trajectory contains a full back-and-forth trip, for visualisation.
You can then setup a small .csh command file to do MR for each of the decoys, in turn, using your favorite MR packake (MolRep, EPMR, Phaser, AMoRe...).

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters)

Trajectory file (e.g. mode_7.pdb):

Input data formats

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

  • The trajectory title is the output of the "Submit a job" option, for one particular normal mode.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 15:37 April 25, 2007.