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· 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
  · Submit a job
  · Include Profit step
· X-Ray refinement
  · Standard refinement
  · Screening Mol. Repl. Solns.
· EM refinement
  · Documents/Examples
  · 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
· References
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· Job queue status

EM Map Structure Factors

The program first performs resectioning and recentering of an input map to make it compatible with FFT by sfall-CCP4 (see Documents).

It then performs FFT and outputs the structure factors that are needed to submit a refinement job.

Your email adress: (Recommended, for notification)


Job title: (Recommended, only alphanumerical characters)


Unit cell parameters (4th line in CNS map header):
- - Edges (Angstr.)
- - Angles (Deg.)

Space group number is supposed to be 1 (P1).

Lowest & highest resolution to use (Ångström):
--

File with observed electron density map Ex: CNS map


Format of observed electron density map
Supported formats are: NEWEZD, CNS, CCP4...

For CCP4 maps use mapsig to display the header...


Sampling of the map (# of grid points along a, b, c)
-- --

Limits of the map (along a, b, c)
-- --


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 map should contain a complete asymmetric unit, as specified in the CCP4 documentation of sfall.
    Whatever the map limits, the program will recenter it to make it compatible with FFT routines... It will also resection it as specified by the user...

  • The sampling NA, NB, NC should be chosen so that one grid point should represent ~ (max_resol/4) Angstroms (i.e. if resolution is 8 Angstrom, the sampling should be less than 2 Angstroms).
    There are some rules to be satisfied concerning NA, NB and NC: thet should not contain among their factors a PRIME number larger than 19; Also, they should be EVEN numbers.
    The sectioning in P1 is supposed to be Z, X, Y.
    See the sfall full documentation on line.



  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 19:08 May 01, 2017.