||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
||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
||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
||Same as protein-RNA. Ligand's flexibility has to be described in a file formatted in certain syntax.
||Protein-protein interface sampling
||Similar to protein-RNA. Loops on each domain close to another are identified and sampled.
||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
||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.