· 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
Refinement of potential Molecular Replacement solutions
Performs refinement of potential Molecular Replacement solutions against X-ray data
along Normal Mode directions of low frequency (including rotations and translations).
The potential Molecular Replacement solutions are specified through a file containing
the eulerian angles of the rotation and the translation vector (in Angstrom).
The first line of the input file is a title while the second indicates how many solutions
are to be refined. See example here.
This version of the program maybe slightly more stable than the "standard refinement" protocol
in that it uses a 1/(omega_k)**2 weighting for normal mode amplitude c_k of mode k.
In addition to PDB structure, the SYMM data file and the HKL data file, you must provide:
- The resolution limits of the data.
- The number of low-frequency modes to use.
- The Rot_and_trans parameters for each model
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.
- The symmetry data is a text file that describes the box and symmetry operators.
On the first line there should be six numbers, representing unit cell dimensions (a,b,c)
in Ångströms and the cell angles (alpha,beta,gamma) in degrees.
They are read in the Fortran format '(6f8.3)'.
This is followed by symmetry operators, using the AMoRe program format. Each operator
is followed by a '*', and the list is terminated with an 'end' record.
If there are more than one line, the program should be able to cope with this.
However, there has been some report of troubleshooting in some cases; if it happens,
make sure each line is terminated by a '*' and fill in
the line with blanks until it reaches 80 characters...
A couple of examples
(you should NOT just copy these):
- The reflection data is a free-format text file with one
reflection per line. Columns are separated by at least one space, and
there are 5 columns per line. The first
three are integers corresponding to the h,k,l indexes. Column 4 is
the amplitude of the reflection and column 5 the error (sigma). Column five
is currently not used, but the code expects a floating-point value to be there.
Reflections outside the low/high limits specified by you will be discarded.
An example: Fobs_example.data.
- The refinement is carried out in reciprocal normal mode space.
Low-frequency modes offer the advantage to allow for collective and large-
In the order of 10 modes should work well for normal proteins, but you
can experiment with higher values, although the execution will be slower.