#Example starts with:

#3fy3.pdb

A rosetta compatible, relaxed pdb. Run in order indicated by #) id

Easy way (skip to step 4 after running)

1-3) make_repeat_structures.py

Slow way (potentially more control)

1. generate_cst.py -pdbs 3fy3.pdb

2. generate_backbones.py -pdbs 3fy3.pdb -repeat 4 -max_turns_per_repeat 2

3. remove_redundant_structures.py -pdb_stem _3fy3

4. expand_cst.py -ref_pdb 3fy3.pdb -ref_cst 3fy3_All.cst -repeat_pdb_tag _3fy3

Be careful and considerate this spawns 10 processes

4. optimize_repeat_structures.py -pdb_stem _3fy3 -thread 10

OR

Now you are also generating silent processes

nohup optimize_repeat_structures.py -pdb_stem _3fy3 -thread 10 > log.txt &

5. score_and_select_2d.py -pdb_glob 'src*_3fy3*.pdb' -native 1M8N_Relax.pdb -name 1m8n_ref

6. reattach_caps.py -ref_pdb 3fy3_Relax.pdb -ref_cst 3fy3_Relax_All.cst -repeat_tag _3fy3_Relax -thread 1

7. score_and_select_2d.py -pdb_glob 'src*_3fy3Cap.pdb' -native 1M8N_Relax.pdb -name 1m8n_ref

#generate_backbones.py

generate_backbones.py -pdbs 3fy3.pdb -repeat 4 -max_turns_per_repeat 2

Give pdb(s) with beta solenoid repeat. Uses Pyrosetta directly and via Daniel Silva's RMSD aligner function in solenoid_tools

#generate_cst.py

Makes cst file for each input pdb. For options see -h. Uses Pyrosetta directly and via SASA wrapper from Alex Ford's interface_fragment_matching for solvation calculation

By default, make contraints for all Nitrogen to Oxygen ( and O to O contacts with at least one hydrogen in the system ) and disulfides.

#expand_constraints.py

expand_cst.py -ref_pdb 3fy3.pdb -ref_cst 3fy3_All.cst -repeat_pdb_tag _3fy3

optional arguments:

-h, --help show this help message and exit

-ref_pdb REF_PDB reference pdb

-ref_cst REF_CST corresponding to reference pdb

-repeat_pdb_tag input pdb tag

-out OUT Output directory

optimize_repeat_structures.py

!!! Be careful and considerate !!!

optimize_repeat_structures.py -pdb_stem _3fy3 -thread 10

OR

!!! Generating silent processes !!!

nohup optimize_repeat_structures.py -pdb_stem _3fy3 -thread 10 > log.txt &

optional arguments:

-h, --help show this help message and exit

-pdb_stem PDB_STEM pdb stem, start of globs for pdbs and csts

-thread THREAD number of parallel threads to run

usage: score_and_select_2d.py [-h] -pdb_glob PDB_GLOB -native NATIVE -out -param [] OUT [-score SCORE] [-plot PLOT] [-norm NORM] [-name NAME]

for plotting pdb scores and selecting subsets based on absolute or per residue scores

score_and_select_2d.py

For -plot function (on by default, 0 for off) you need a plotly account from https://plot.ly/python/. Github accounts work. You must provide

optional arguments:

-h, --help show this help message and exit

-pdb_glob pdb stem, start of globs for pdbs and csts

-native_pdb pdb to compare designs against

-out OUT folder to move files to

-score SCORE select all structures with less than this REU /

               residue

-plot PLOT 0|(1) plot scores with plotly

-norm NORM 0|(1) normalize scores by residue

-name NAME plot tag

#reattach_caps.py reattach_caps.py -ref_pdb 3fy3_Relax.pdb -ref_cst 3fy3_Relax_All.cst -repeat_tag _3fy3_Relax To trim off residues (i.e. not use full length protein before/after duplicated region as cap) provide args like: reattach_caps.py -ref_pdb 3fy3_Relax.pdb -ref_cst 3fy3_Relax_All.cst -repeat_tag _3fy3_Relax -n_trim 48 -c_trim 24 -step 24 the above example will trim off 0, 24, and 48 residues off the end of the n-terminal cap and 0 & 24 residues off the beginning of the c-terminal cap

Misc other scripts

cst_to_pymol.py

cst_to_pymol.py -cst 3fy3_All.cst

use to visualize cst file in pymol (copy paste output into pymol session with pdb corresponding to cst file)

repeat_search.py

Use to find repeat motifs involving particular residues, i.e. aromatics, charges, etc. Bias toward favored residues in a amino acid matirx like in matrix.tsv.

script needs to be in directory with repeatdb.txt (included in repo) which contains data from repeatsdb.bio.unipd

optional arguments:

-h, --help show this help message and exit

-pdbs PDBS pdb ID list to check

-output OUTPUT output directory

-aa_matrix weight matrix for amino acid types to rank repeat rows

                    based on desired amino acid composition

-repeat_class type of repeat a la repeatsdb.bio.unipd, e.g. "III.1"

-dist_targ neighboring repeat target spacing

-dist_flex neighboring repeat spacing flexibility

-angle_flex maximum cosine (in degrees) difference between

                    displacement vectors considered repeatative

-min_repeats mimium number of repeats to record

-min_aa_score minimum AA composition sum based on scores in matrix

-min_sasa minimum average residue sasa value for reported

                    repeats

-max_sasa maximum average residue sasa value for reported

                    repeats

-sasa_probe_radius probe radius for sasa calculations

Baker lab usage

Simplest (I think) use in-lab as follows:

export PYTHONPATH=/work/pylesh/python_local.bak:$PYTHONPATH

source /work/pylesh/virtualenvs/dev/bin/activate