|
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 kept privat
(remember to keep track of your job-id).
To make jobs visible to everyone via the
job status
page, untick the
checkbox below.
keep my job private
|
If you wish to be notified by e-mail once your job is finished,
enter your e-mail address into the field below
(recommended if your job is kept private). Your e-mail
will never be shown on the internet and is used ONLY
to notify you about your job status.
If you enter a pseudonym (any name without a @ character), this will
be used to identify your jobs on the
job status
page.
pseudonym or e-mail, 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 changes 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).
|
|
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 changes.
|
|
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) |
|
|
