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Should you encounter any unexpected behaviour,
please let us know.

Submit a job to elNémo !

Basic options
elNémo will compute ten perturbed models for the first five non-trivial normal modes of your protein (in PDB format). You may also visualize the collectivity of the atom movement for the first 100 normal modes. Only records starting with the keyword "ATOM" will be considered. Water molecules (HOH, H2O, TIP3 and WAT) will be ignored.

upload a PDB file
or paste your structure information into the field below
You may enter a name for your job here. It will be used as a title for all output and to identify your job on the job status page.
job identifier, optional
By default, all jobs are visible to everyone via the job status page. However, if you wish your job to be kept private, activate the checkbox below.
keep my job private
If you keep your job private, please note its job-id carefuly. Indeed, since its relocation, elNémo do not send e-mails any more. We hope to make this feature available again in the future.
pseudonym, optional

If this is the first time you are using this site, the default settings of the advanced options below should probably be fine !

Supplementary options for the calculation of NMA perturbed models
Once the normal modes are computed, The Elastic Network Model will compute models that are perturbed with a given amplitude DQ in the direction of a single normal mode. Here, this is done for a range of perturbations (between DQMAX and DQMIN with step size DQSTEP). You may choose the number of modes (starting from the first non-trivial mode 7) and the parameters of the amplitude perturbation. The result will be one PDB file per normal mode, containing the requested NMA perturbed models. These PDB files can be viewed (e.g. using VMD) to follow the conformational change that are induced by the selected mode. They also represent potential templates for molecular replacement searches (see examples). Note that you may still compute more perturbed models once this run has finished).
NMODES= number of lowest frequency normal modes to be computed
DQMIN= minimum perturbation
DQMAX= maximum perturbation
DQSTEP= step size between DQMIN and DQMAX
generate animated gif images (takes about 3 minutes per mode to complete)

Advanced options for comparing two conformations
If a protein structure is known in two different conformations, The Elastic Network Model may be used to determine the contribution of each normal mode to its conformational change.
upload a second PDB file
or paste your structure information into the field below
compute RMSD between structures
project difference vectors on eigenmodes (both PDB files must have identical atom numbering)

Expert options for computing the eigenmodes
Do not change these settings unless you know what you are doing.
NRBL number of residues to be grouped together by diagrtb (by default, NRBL will be determined automatically as a function of protein size to optimize computation speed); select 'diagstd' to deselect RTB (slow!)
CUTOFF cutoff used to dentify elastic interactions (default = 8)

If you find results from this site helpful for your research, please cite one of our papers:

elNémo is maintained by Yves-Henri Sanejouand.
It was developed by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: 20 June 2014.