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Protein Structure Modelling  
Cα-trace Modelling
A Cα-trace modeling is similar to ab initio loop modeling with the additional restraint that the model follow the Cα atoms of your input PDB file. It is an effective method for controlled sampling around an approximately correct structure. If the PDB structure is believed to be very accurate, the model sidechains can be restrained to lie near the PDB sidechains, as enforced by a restraint on the spatial position of the sidechain centroid. The input PDB file should contain all atoms for the region to be modelled, as RAPPER will derive the Cα and sidechain centroid restraints from the atomic coordinates in the PDB file. Unlike loop modelling, Cα models can be generated accurately for arbitrarily long sequences of residues.
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Job name:
PDB file:   (max. 20 MB)
Residues to model:
Chain ID: (Note that this is case-sensitive!)
Start at residue:
Stop at residue:
Number of models to generate:  (only 50 recommended)
Advanced Options
Cα-restraint size Å (The size of the Cα restraint sphere) Values below 2.0 may be difficult to model, especially with sidechains enabled, and may result in model building failures. If you use tigher values and no models are generated, loosen up these restraints.
Enforce sidechain centroid restraints? (Should the model sidechain be enforced to lie near the submitted PDB sidechain atoms?)
Sidechain centroid restraint size Å (The size of the Cα restraint sphere)
Enable new divide and conquer algorithm? (Vastly improves the performance of RAPPER modeling, but may introduce minor chain joint distortions without energy minimization. Important for large proteins)
Anchor Geometry Optimizer Options
Enable optimization? Another geometry optimizations are now disabled in RAPPER
Compute all-atom statistical potential? Always computed
Compute molecular mechanics potential energy?  (Highly recommended, but will take some time)
Enable GB/SA continuum solvation? (Highly recommended)
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