· 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
· 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
Normal mode calculation and visualisation
You need at least one pdb file to calculate Normal Modes using the Elastic Network Model, plus a couple of parameters
described at the bottom of this form.
Choose the number of modes you want, provided that there are less than 106 (=100+6); that is only to save some of our disk space:
if you want more, please send us an e-mail.
The scale (amplitude) of the movement can be chosen by controlling the average rmsd of the trajectory (see below).
The rmsd per residue is given on output for each chosen mode (as a plot).
There will be one output PDB file per mode, named mode_#.pdb, directly loadable by PyMol or
VMD: this is a concatenation of 30 PDB files separated by an ENDMDL card.
This PDB file maybe split into 30 pieces for Molecular Replacement.
There is also a tarred file with all modes.
As a bonus, you will get a file loadable by Pymol to generate a picture of the Elastic Net associated to your protein
1GGG.pymol (thanks to Patrice Koehl).
Finally, there will be the modes.dat file that contains, for each mode, its frequency and eigenvector list, for your personal use.
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 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). The length of each mode vector will be 3*natoms.
It is not recommanded to include Hydrogen atoms in the PDB file.
- All interactions are weighted by exp(-(d_ij(0)/d_0)^2), where d_0 is a
This effectively introduces a smoother "cutoff" value than in the original Tirion model.
A value of 3.0 Angstrom works well for CA-only
models, but you might prefer a larger value (5.0-10.0 Angstrom) for
See the Hinsen article in the References section.
- A cutoff is used in the mode calculation. In the Tirion model
(Elastic Network Model) only those pairs of atoms that are closer than
the cutoff are linked by a spring of universal length. Ideally this should
be choosen so that the weighting causes the interactions to be negligible
outside the cutoff, but in practice a cutoff around 10 Angstrom works
fine in almost all cases. In general you might be able to use a smaller
cutoff value for all-atom calculations than CA-only calculation.
See the Tirion article in the References section.
- You can choose how many modes to calculate. The execution time for the
sparse matrix solver is more or less proportional to the number of modes
requested, while the full matrix solver execution is dominated by the reduction
to tridiagonal form - the actual mode calculation is very fast in that case.
Due to the memory requirements you cannot use the full solver for more than
about 5000 atoms, and the sparse solver is much faster even for small systems
(from about 500 atoms) if you only want the first (lowest-frequency)
10-100 modes. Remember that the first six modes correspond to rigid body
motions (translation and rotation), so the structurally interesting ones
begin at 7.
You should check in the log file that the first 6 modes have an eigenvalue close to zero.
- If you really want to you can override the automatic choice and specify
either the sparse or full solver. Be aware that the full solver wont work
for more than 5000 atoms, but it is faster for small systems or if you
want a large number of mode vectors (or if you wanted a huge cutoff for some reason).
- Some timing examples for 1ANF with 2860 atoms (Hessian dimension is 8580 by 8580):
Calculating 20 modes takes 33 seconds and for 100 modes it increases to 1 minute and 40 seconds.