bgsu-3D-processing

Repository to store scripts for structure processing from BGSU RNA 3D motif atlas.

Downloading the data from RNA 3D motif atlas

Open http://rna.bgsu.edu/rna3dhub/. Then go to RNA 3D Motif Atlas > Home > Internal Loops > Download > json. The version that I used was 3.78

Download the structures from RNA Solo

Run python download_pdbs.py --json data/il_3.78.json --output_dir pdbs

Get list of all ILs, HLs with all nucleotides included

For each PDB ID you can download the list of internal loops with ALL nucleotides.

Note: The json files contains residue numbers that create a loop but do not include the residues that bulge out of the loop. To build the full atomic model we need all residues The example link for 6UFG lokks like this: http://rna.bgsu.edu/rna3dhub/loops/download_with_breaks/6UFG

Run python download_pdbs.py --json data/il_3.78.json --csv_only --output_dir pdbs_csvs

Run RNAComposer to generate the structures

Renumber the motifs that you want to use and generate *.dot files

For this purpose generate the commands to run RNAqua or RNA-tools. The command should look like this: process_for_RNAqua.py --directory pdbs_csv/ --output_dir RNAtools --rna-tools

The parameter --rna-tools is used to generate the command for RNA-tools. If you want to use RNAqua, just remove the parameter. For my usage I used RNA-tools option. However, this required modified version of RNA-tools script. The original one after donwload has a bug, which was fixed by me. Another problem is that the PDB files remain big and RNA-Composer process these files significantly longer.

You can use RNAaqua, but for some files I had a problem with the output. In some cases the output zip file was corrupted and could not be used. The were two main reasons for this:

1. The files contained some non-standard characters in the file names. This was fixed by replacing '-' with '_'.
2. Some files names contain incorrect chain id, e.g. 1XYZ_C, while the chain id in file is A.

This command will also generate *.dot files, required for RNA-Composer, with GNRA loop added to the structure and additional GC pairs.

The output processed for RNAaqua is in zip format, so then use ./unzip_all_files.sh to unzip all files.

Generate sbs files

Once the renumbered pdb files are generated you can run script prepare_sbs.sh to generate sbs files. The script will generate sbs files for each pdb file in the directory. The *.sbs and *.dot files are required for RNA-Composer in the next step.

(Optional) Transfer files to the server

You can use rsync to transfer the generated sbs files and dot files to the server. The command should look like this: rsync -av sbs_files/ user@server:/path/to/sbs_files

(Optional) Fix file names

Note that RNA-Composer does not accept '-' in the file names. You need to replace '-' with '_'. For this purpose I used the following command: rename 's/-/_/g' * or python fix_names.py <path>

Run RNA-Composer

You can now run RNA-Composer on server. Run the following command: ./run_composer.sh