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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 choose:

  • The resolution limits of the data.
  • The number of modes to use (increasing frequency order).

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters)

PDB file with structure to refine: Ex: PDB
The default here is to use the RTB method with 1 block per residue, therefore all atoms of the PDB file are recommended.

SYMM file with unit cell and symmetry operators: Ex: SYMM

HKL file with obs. X-ray reflections: (max 50,000 refl.) Ex: HKL

ROT file with initial orientation and translation Ex: ROT

Lowest & highest resolution to use (Ångström):

Lowest and highest normal modes to 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.

  • 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- amplitude movements. 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.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 10:29 November 19, 2007.