The scripts and input files that accompany this demo can be found in the demos/public directory of the Rosetta weekly releases.

KEYWORDS: INTERFACES GENERAL

Author: Kevin Houlihan (khouli at unc dot edu)

This demo contains scripts to redesign residue sequences at the interface of existing heterodimers. Protocols for running with PackRotamers, MinMover, and MinMover with a scorefunction produced by optE are included.

## Setup

This demo contains scripts with absolute paths that need to be updated. A script is included to do this for you. (If you don't want to use it a list of files with absolute paths that need to be set is at the bottom of this section.)

Run the configure script. Pass your rosetta directory as an argument if it isn't in your home directory. After setting your rosetta directory, the script tries to add a weight file.

Example:

[khouli@killdevil-login2 demo]$./configure Use /nas02/home/k/h/khouli/rosetta as Rosetta directory for scripts? [Y/n]y /nas02/home/k/h/khouli/rosetta Add optE_inf_premin.wts to /nas02/home/k/h/khouli/rosetta/rosetta_database/scoring/weights/? [Y/n]y  Alternatively: [khouli@killdevil-login2 demo]$ ./configure other_dir/rosetta
other_dir/rosetta


This fixes absolute filepaths within the interface_design_demo/ directory. Adding the optE_inf_premin.wts to your weights folder is necessary for the protocol in scripts/design/minpac_optE_premin/ to run.

The configure script makes a few assumptions. You may want to change these. What those assumptions are and where they can be found:

• The relative paths downwards from interface_design_demo/ have not been changed e.g. scripts within the demo can access other scripts within the demo at their expected paths

rosetta_database/: referenced by design scripts, e.g. pacrot_s12p_nomin.sh (run by run.sh)

rosetta_source/bin/sequence_recovery.linuxgccrelease: referenced by scripts/analyze/seqRec.sh (run by infpro.sh)

rosetta_source/bin/rosetta_scripts.mpi.linuxgccrelease: referenced by design scripts referenced by scripts/analyze/seqRec.sh (run by infpro.sh)

• Your mpi system is the same as mine and you want to use the same options referenced in design scripts

This can also be done manually. Files with absolute paths:

• design scripts in /scripts/design/ e.g. scripts/design/pacrot_s12p_nomin/pacrot_s12p_nomin.sh

• scripts/analyze/seqRec.sh

• inputs/selected_chains/selected_chains.list

• inputs/min_nats/nats.list

## Running Design Protocols

From within one of the protocol directories in scripts/design/, run the run.sh script.

What this script is doing:

This script runs the actual design script (the one with the same name as the directory) and passes it 3 arguments. The first argument names the job after the directory (and hence creates an identically named sub-directory with output pdbs), the second passes selected_chains.list as the list of proteins to use, and the third passes the name of the .xml file containing the Rosetta Script to be used.

Example:

[khouli@killdevil-login2 pacrot_s12p_nomin]$pwd /nas02/home/k/h/khouli/interface_design_demo/scripts/design/pacrot_s12p_nomin [khouli@killdevil-login2 pacrot_s12p_nomin]$ ./run.sh
Group   (-G) : bkuhlman_pi
Project (-P) : bkuhlman_pi
Memory Limit (-M) : 4 GB
Job <287057> is submitted to queue <day>.


Change Rosetta run parameters within the .sh script file. Change the protocol described by the Rosetta script in the xml file. Interface residues are determined by the RestrictToInterfaceVector task operator in the Rosetta script.

## Analysis

Once a design run completes, analyze it by running post_run.sh from the same directory the run.sh script was executed it. Inside the output directory, this will generate the files top_interface_score, sequence_recovery.txt, and submatrix.txt as well as some others of much less interest.

What this script is doing:

This script is a convenient way to execute the script interface_design_demo/scripts/analyze/infpro.sh with the proper working directory. ../../../analyze/infpro.sh from within the output directory is awkward.

In turn, infpro.sh is runs a script to score interfaces of output pdbs, identify the best trajectories of each protein based on those scores, and then runs a script to analyze sequence recovery and to aggregate substitutions in residues between the inputs and designs.

This script assumes your rosetta path contains:

rosetta_source/bin/sequence_recovery.linuxgccrelease


This can be changed in scripts/analyze/seqRec.sh.

To run infpro.sh, set the directory that conntains the output pdbs as your working directory and then run interface_design_demo/scripts/analyze/infpro.sh.

Example:

[khouli@killdevil-login2 pacrot_s12p_nomin]$pwd /nas02/home/k/h/khouli/interface_design_demo/scripts/design/pacrot_s12p_nomin/pacrot_s12p_nomin [khouli@killdevil-login2 pacrot_s12p_nomin]$ ls sequencerecovery.txt
ls: sequencerecovery.txt: No such file or directory
[khouli@killdevil-login2 pacrot_s12p_nomin]$~/interface_design_demo/scripts/analyze/infpro.sh [khouli@killdevil-login2 pacrot_s12p_nomin]$ ls sequencerecovery.txt
sequencerecovery.txt


The outputs worth looking at are sequence_recovery.txt, submatrix.txt, and top_interface_scores.

## Example ouputs

The directory example_outputs/ contains outputs generated by running the configure script and then running each protocol as described above. Each protocol produces one output folder as well as a benchmark.txt file. The benchmark.txt files have been prefixed with their protocol but otherwise all outputs are exactly as produced within the scripts/design/name_of_protocol/ directories.

## Where to change parameters

In the run.sh file for the design, change the variable $input_pdb_list to the filename of a text file containing a list of pdbs to use as inputs. Alternatively, add pdbs to inputs/selected_chains/ and re-run configure. The new pdbs will be added to inputs/selected_chains/selected_chains.list Either way, if you want sequence recovery to function you'll need to add a corresponding structure to the set used for sequence recovery. • Adding/removing native structures for sequence recovery: In the post_run.sh file for the design, change the assignment of$native_pdb_list to the filename of a text file containing a list of pdbs to use as natives. Alternatively, add pdbs to inputs/min_nats/ and re-run configure. The new pdbs will be added to inputs/min_nats/nats.list. If you want sequence recovery to function you'll need to have added a corresponding structure to the set used for input. (They have to align by simple ls, i.e. cap-sensitive non-numerical alphabetical order).

• Number of trajectories used for sequence recovery:

In the run.sh file, change the n_traj assignment at the top.

• Options passed to Rosetta and MPI:

In a protocol directory, edit name_of_protocol.sh

## Troubleshooting

PMGR_COLLECTIVE ERROR following post_run.sh: Fix the path to the sequence_recovery binary in interface_design_demo/scripts/analyze/seqRec.sh

## Epilogue

Happy Rosetta-ing!