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Protein Structure Modelling  



    Each directory in rappertk/tests is an illustration of rappertk applied to some problem. Additionally it contributes a testcase to the testsuite (executed by 'make tests'). testscr file in every directory of in rappertk/tests/ contains the command and README contains explanation.
    Note that electron density restraints can be applied in almost every case optionally.
    Following is a listing of examples in rappertk/tests with brief description.

    Task Directory Description
    CA tracing catrace If you know approximate location of CA atoms and sidechains in a poypeptide, use this command to trace your structure through those restraints. Trace can be done in forward or reverse directions, in a simple or restraint-guided way, and with or without sidechains.
    CA tracing in electron density xcatrace This is similar to catrace, but a map or mtz can be provided to put electron density restraints. Strictness of electron-density restraints can also be specified.
    Protein-RNA interface sampling protrna Protein loops close to RNA are identified. Both RNA and protein are then sampled within the specified positional restraints. Can be done within electron density also.
    Protein-ligand interface sampling protlig Same as protein-RNA. Ligand's flexibility has to be described in a file formatted in certain syntax.
    Protein-protein interface sampling ppi Similar to protein-RNA. Loops on each domain close to another are identified and sampled.
    Loop building loop There is a loop closure procedure which closes the loop. Can be executed within positional and Xray restraints.
    Sampling in simulated EM data using secondary structure ssEM This is actually a secondary-structure-sensitive way of CA-tracing. Secondary structure has to be provided in a file formatted to a particular syntax. Additionally electron-density can be provided as map file, along with positional reatraints. Loops are excluded from positional restraints.

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