CCCP 
 CCCP (Coiled-coil Crick Parameterization)
This program fits a set of generalized Crick parameters1,2 given a coiled-coil structure. Contact gevorg.grigoryan at gmail dot com with bug reports or requests requests for additional features.

PDB File:      OR     PDB ID:

Coiled-coil region*: (PyMOL-style selection)

Allow for variable-length chains
Align input onto ideal fit (in standard frame) instead of ideal onto input



Optimization settings:
Global:
We recommend trying this setting first. It assumes nothing about the symmetry of the structure, allowing each chain to have its own super-helical phase offset and Z-offset. By analyzing the best-fit parameters, one can determine whether the structure actually has any kind of symmetry.
Vary minor helix phases independently
Global symmetric
At most one Z-offset and one variable super-helical phase offset is allowed, which relate all up chains to all down chains. For parallel topologies this results in Cn symmetry (n is the number of chains). For alternating up/down topologies, this results in Dn symmetry. And for all other topologies super-helical phase offset between adjacent chains is set to 2π/n and only one Z-offset is allowed for all up chains relative to all down chains.
Seeded:
Specify a starting point for the optimizer that you think might be close to a good solution if you get an unreasonable solution otherwise (and you think better solutions exist).
Parameter (symbol, unit) Starting Point
Superhelical radius (Ro, Å):
α-helical radius (R1, Å):
Superhelical frequency (ωo, °/aa):
(negative means left-handed superhelix)
α-helical frequency (ω1, °/aa):
Pitch angle (α, °):
α-helical phase (φ1, °):

Impose superhelical phase symmetry
Allow only one z-offset (all up chains are offset relative to all down chains by the same amount)



* all residues must at least have a CA atom

1 F. H. Crick, "The Fourier Transform of a Coiled Coil", Acta Cryst., 6: 685 (1953)
2 G. Grigoryan, W. F. DeGrado, "Probing Designability via a Generalized Model of Helical Bundle Geometry", J. Mol. Biol., 405(4): 1079-1100 (2011)