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· 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
· 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
· Job queue status
Calculate Normal Modes Overlap Coefficient
(Needs 2 PDB structures)
In this version, there is no need to have previously superimposed the 2 PDB files.
The superposition will be done locally by Profit.
Obviously, the two PDB files should have the same number of (CA) atoms.
- The PDB files should contain only CAs ; They should have exactly the same number of residues.
The superposition will be done by Profit.
The calculation will not work efficiently for PDB files with more than 3000 CA atoms.
In this case, one should resort to the RTB method and work with Blocks of residues (YHS).
Go and visit Elnemo web site for a web-interfaced implementation of this
(see Links option).
- The output files will consist of 2 postscript files showing the overlap coefficients (dot product)
between the eigenvectors of the first 100 lowest-frequency modes and the set of difference vectors between
the two forms.
As a check, the contribution of the first 6 modes should be exactly zero, if the superposition has been done correctly.
The calculation is done twice: once while using the first form to calculate the normal modes and another time
while using the second form to calculate the normal modes.
N.B. The cumulated score is also shown.
- The job title is for internal use only, but note that
it will show up in the public job queue (but your results will not be public).
Avoid using a blank line here, otherwise the second plot will not be named properly and you won't be able to download it.