Spruce Output Naming Conventions

Output files generated from Spruce follows a general naming scheme.


The scheme can be prefixed by the user using the -prefix input parameter. The user can also control the output to a single file using the -out, and additionally, set -warts to append “_#” to the user specified output name.

Example of a structure without an alternate location, 2 files generate due to two ligand sites detected:



Example with an alternate location code:


For apo structures, the residue named is the one closest to the center of the marked binding site. This is irrespective of whether a different residue was input to spruce to indicate the location of the binding site. Apo pocket example:


Peptidic ligand example, where the ligand section is named slightly differently following the scheme chainID-StartingResidueNumber-1LetterCodes-EndingResidueNumber. Only standard residue get 1 letter codes, whereas non-standard residue will have 3 letter codes separated by dashes.