Author: Andrew Watkins (amw579@stanford.edu)
Last updated July 4, 2017; PI: Rhiju Das (rhiju@stanford.edu).
rosetta/main/source/src/apps/public/dump_capped_residue.cc
rosetta/main/tests/integration/tests/farfar_mrna
rosetta/main/tests/integration/tests/read_polymeric_components
Exporting a PDB file of a given residue -- which can be specified via Rosetta nomenclature (i.e., the base name followed by a colon-separated list of patches).
BuildPeptide requires no particular input files.
| Flag | Description | Type |
|---|---|---|
| -dumper:residue_name | Full or base name of the desired residue | string |
| -nopatch | (optional) If true, don't add polymeric capping groups | bool |
| -fiveprime | (optional) If RNA, add the FIVEPRIME_CAP variant and also instantiate a 7-methyl guanosine, then optimize the connected geometry. | bool |
It's a great idea to run this application as you construct a params file for a new residue type, so you can visualize what it looks like. Finally, you may want to use this application to prepare a capped PDB file for QM optimization.
The output of a dump_capped_residue run is a PDB-format file of the residue in an extended full-atom conformation.