Usage: ./CompAnnotate REFERENCE-PDB-ID ChainId TARGET-PDB-ID ChainId [-m method-name] [-f original]
Here the PDB-IDs are expected to be the 4 character id of PDB files, and the ChainIds are expected to be single character chain id. The parameters inside the brackets are optional. Preferred input annonation methods than the default MC-Annotate can be chosen using [-m method-name] option. The output data and format can be changed from default '.rca' format to get the original format of MC-Annotate and RNAView using [-f original] option, when input annotation is MC-Annotate and RNAView correspondingly.
For this method, it is necessary to provide PDB file and one or more annotation files from MC-Annotate, RNAView, FR3D, 3DNA/DSSR or ClaRNA annotation output according to user's need and preference. Providing alignment files are optional but recommended. The sequence information is included in the package, but might require update from PDB server, for newly added sequences.
[Note: The details of the command options and input data are given in the 'README' file included in the package.]