Preliminary information and input/output file processing

Using Rosetta applications

Rosetta programs (executables) re located in your main/source/bin directory. Each application name has an extendion, denoting compilation platform and variant. For example, programs compiled on mac with clang the extension is .macosclangrelease, while compiled on Linux with gcc - .linuxgccrelease

Idealising input PDB file for Rosetta

The following command reads in a PDB file and writes that protein in an ideal form, i.e. with all bond lenghts and planar angles according to the Rosetta definition. Next step - run “idealize_jd2” program as follows:

idealize_jd2.macosclangrelease -in:file:s 1tenA.pdb

Extract PDBs from an output silent file

Silent file (.out file) produced by Rosetta may be converted into a set of separate PDB files with extract_pdbs program:

extract_pdbs.linuxgccrelease -in:file:silent default.out -out:prefix ./out_pdb/

where out_pdb is the name of output directory which must exist (Rosetta does not create it on her own)

To extract only selected frames, use: -in::file:tags:

extract_pdbs.linuxgccrelease -in:file:silent default.out -out:prefix ./out_pdb/ -in::file:tags S_00001234 S_00000123