This directory contains files for a loop-lengthening example.

The starting point is 1FNA_repacked.pdb.  This is basically the same as 1FNA.pdb from the PDB, except it's been massaged in Rosetta ahead of time; the changes are not relevant to this example but included renumbering residues from 1 and repacking.

An alanine in the BC loop is cut-and-paste-duplicated repeatedly, followed by PDB renumbering (and deletion of the score information at the end), to make 1FNA_preextend.pdb.

In 1FNA_repacked.pdb, we have alanine 21:

ATOM    303 2HG  PRO B  20     -10.756  27.345  15.165  1.00  0.00              
ATOM    304 1HD  PRO B  20      -9.805  25.177  16.540  1.00  0.00              
ATOM    305 2HD  PRO B  20      -8.702  26.291  15.722  1.00  0.00              
ATOM    306  N   ALA B  21     -10.917  28.859  19.893  1.00  0.00              
ATOM    307  CA  ALA B  21     -11.787  28.893  21.073  1.00  0.00              
ATOM    308  C   ALA B  21     -13.181  28.310  20.831  1.00  0.00              
ATOM    309  O   ALA B  21     -13.875  27.964  21.816  1.00  0.00              
ATOM    310  CB  ALA B  21     -11.907  30.323  21.579  1.00  0.00              
ATOM    311  H   ALA B  21     -10.690  29.703  19.451  1.00  0.00              
ATOM    312  HA  ALA B  21     -11.373  28.228  21.831  1.00  0.00              
ATOM    313 1HB  ALA B  21     -12.536  30.342  22.468  1.00  0.00              
ATOM    314 2HB  ALA B  21     -10.917  30.706  21.827  1.00  0.00              
ATOM    315 3HB  ALA B  21     -12.354  30.946  20.806  1.00  0.00              
ATOM    316  N   VAL B  22     -13.539  28.234  19.588  1.00  0.00              
ATOM    317  CA  VAL B  22     -14.858  27.768  19.131  1.00  0.00              
ATOM    318  C   VAL B  22     -14.842  26.327  18.633  1.00  0.00              
ATOM    319  O   VAL B  22     -13.802  25.813  18.272  1.00  0.00              

In 1FNA_preextend.pdb, it appears 4 times, with the PDB numbering repaired:

ATOM    303 2HG  PRO B  20     -10.756  27.345  15.165  1.00  0.00            
ATOM    304 1HD  PRO B  20      -9.805  25.177  16.540  1.00  0.00            
ATOM    305 2HD  PRO B  20      -8.702  26.291  15.722  1.00  0.00            
ATOM    306  N   ALA B  21     -10.917  28.859  19.893  1.00  0.00            
ATOM    307  CA  ALA B  21     -11.787  28.893  21.073  1.00  0.00            
ATOM    308  C   ALA B  21     -13.181  28.310  20.831  1.00  0.00            
ATOM    309  O   ALA B  21     -13.875  27.964  21.816  1.00  0.00            
ATOM    310  CB  ALA B  21     -11.907  30.323  21.579  1.00  0.00            
ATOM    311  H   ALA B  21     -10.690  29.703  19.451  1.00  0.00            
ATOM    312  HA  ALA B  21     -11.373  28.228  21.831  1.00  0.00            
ATOM    313 1HB  ALA B  21     -12.536  30.342  22.468  1.00  0.00            
ATOM    314 2HB  ALA B  21     -10.917  30.706  21.827  1.00  0.00            
ATOM    315 3HB  ALA B  21     -12.354  30.946  20.806  1.00  0.00            
ATOM    316  N   ALA B  22     -10.917  28.859  19.893  1.00  0.00            
ATOM    317  CA  ALA B  22     -11.787  28.893  21.073  1.00  0.00            
ATOM    318  C   ALA B  22     -13.181  28.310  20.831  1.00  0.00            
ATOM    319  O   ALA B  22     -13.875  27.964  21.816  1.00  0.00            
ATOM    320  N   ALA B  23     -10.917  28.859  19.893  1.00  0.00            
ATOM    321  CA  ALA B  23     -11.787  28.893  21.073  1.00  0.00            
ATOM    322  C   ALA B  23     -13.181  28.310  20.831  1.00  0.00            
ATOM    323  O   ALA B  23     -13.875  27.964  21.816  1.00  0.00            
ATOM    324  N   ALA B  24     -10.917  28.859  19.893  1.00  0.00            
ATOM    325  CA  ALA B  24     -11.787  28.893  21.073  1.00  0.00            
ATOM    326  C   ALA B  24     -13.181  28.310  20.831  1.00  0.00            
ATOM    327  O   ALA B  24     -13.875  27.964  21.816  1.00  0.00            
ATOM    328  N   ALA B  25     -10.917  28.859  19.893  1.00  0.00            
ATOM    329  CA  ALA B  25     -11.787  28.893  21.073  1.00  0.00            
ATOM    330  C   ALA B  25     -13.181  28.310  20.831  1.00  0.00            
ATOM    331  O   ALA B  25     -13.875  27.964  21.816  1.00  0.00            
ATOM    332  N   VAL B  26     -13.539  28.234  19.588  1.00  0.00            
ATOM    333  CA  VAL B  26     -14.858  27.768  19.131  1.00  0.00            
ATOM    334  C   VAL B  26     -14.842  26.327  18.633  1.00  0.00            

Notice the coordinates are nonsense, all the alanines are atop each other.

We repair this lengthened loop with loop modeling, using the loop_modeling executeable and the included options file.  The included fragments file and loops file allow for the build_initial mode of loop modeling, which deletes the loop conformation and makes a new one from scratch with fragments and CCD.  This mode does KIC refinement but it's hardly necessary.
