- Example
To create a RIN from all chains (and ligands) of a protein in a PDB file, execute the shell command:
INST_DIR/RINerator_V0.5.X/Source/get_chains.py path_pdb path_output path_chains [path_ligands]
Parameters:
- path_pdb: PDB file or directory containing PDB files of the same protein structure
- path_output: directory to save generated files
- path_chains: file with chain identifiers separated by commas
- chain identifier might be any letter or an empty string
- examples: "A,B,I" or "" or "A,"
- path_ligands: [optional] file with ligand identifiers separated by new lines
- each ligand is listed with a name, a chain identifier and a residue number separated by commas
- examples: "NOA,I,1" or "NOA,,1"
Test command from within the RINerator_V0.5.X directory:
Source/get_chains.py Test/PDB/pdb1hiv.ent Test/Results/ Test/INPUT/chains_1hiv_all.txt Test/INPUT/ligands_1hiv_all.txt
- Example
To create a RIN from a specific selection of residues in a PDB file, execute the shell command:
INST_DIR/RINerator_V0.5.X/Source/get_segments.py path_pdb path_output path_segments [path_ligands]
Parameters:
- path_pdb: PDB file or directory containing PDB files of the same protein structure
- path_output: directory to save generated files
- path_segments: file with segment identifiers separated by new lines
- each segment consists of a model number, a chain identifier, a starting and ending residue number separated by commas
- starting and ending residue numbers should be one of these:
- number: residue number
- _: should be set both as starting and ending to consider all residues in the chain
- None: could be set as ending residue if there is only a starting residue available
- examples: "0,A,_,_" or "0,B,25,None" or "0,B,50,70"
- path_ligands: [optional] file with ligand identifiers separated by new lines
- each ligand is listed with a name, a chain identifier and a residue number separated by commas
- examples: "NOA,I,1" or "NOA,,1"
Test command from within the RINerator_V0.5.X directory:
Source/get_segments.py Test/PDB/pdb1hiv.ent Test/Results/ Test/INPUT/segments_1hiv.txt Test/INPUT/ligands_1hiv_all.txt
- Example
To calculate conservation scores from a user-specified MSA file, execute the shell command:
INST_DIR/RINerator_V0.5.X/Source/get_conservation.py gap_format output_format path_alignment path_out path_log [path_id]
Parameters:
- gap_format: any symbol will be considered as a gap
- output_format:
- name+score: identifier conservation_score
- resid+score: index conservation_score
- score: conservation_score
- path_alignment: file with multiple sequence alignment in FASTA format
- path_out: file with 1 or 2 columns (according to output_format) separated by space
- path_log: log file
- path_id: [optional] file with nodes identifiers (according to the NONgaps positions in the first sequence in alignment) in TXT format (should not contain empty lines)
Test command from within the RINerator_V0.5.X directory:
Source/get_conservation.py - name+score Test/INPUT/pdb1hiv_ConsrufDB_align.fasta Test/Results/pdb1hiv_h_cons.txt Test/Results/pdb1hiv_h_cons.log Test/OUTPUT/pdb1hiv_h_res.txt
Note that we use the Test/OUTPUT/pdb1hiv_h_res.txt identifier file since it contains *only* the residue nodes from chain A in contrast to Test/Results/pdb1hiv_h_res.txt, which currently contains all residue nodes assuming the previous test commands were executed.
- Example
To retrieve data from external resources, such as AAindex and ConSurfDB, execute the shell command:
INST_DIR/RINerator_V0.5.X/Source/get_data.py path_id path_output pdb_id [path_input]
Parameters:
- path_id: file with nodes identifiers (according to the RIN specifications) in TXT format
- path_output: file to save retrieved data
- pdb_id: PDB identifier
The script will try to retrieve the conservation scores from the ConSurfDB website, if no consurf.grades files are found in path_input.
- path_input: [optional] path with additional input data, any of the following files will be considered:
- consurf.grades: conservation scores from ConSurfDB
If more than one file, e.g., for each chain, the chain identifier should be included in the file name: consurf_A.grades
- *.sif: network file generated by RINerator
This file will be used to calculate the number of unweighted residue interactions of each residue node.
- *_nrint.ea: edge attributes generated by RINerator
This file will be used to calculate the number of atomic interactions of each residue node.
- *_intsc.ea: edge attributes generated by RINerator
This file will be used to calculate the sum of atomic interaction scores for each residue node.
Test command from within the RINerator_V0.5.X directory:
Source/get_data.py Test/Results/pdb1hiv_h_res.txt Test/Results/pdb1hiv_h_data.na 1hiv
So far, the following data are retrieved:
- ConSurfDB: conservation scores from the ConSurfDB
- FAUJ880111: AA positive charge
- FAUJ880112: AA negative charge
- GRAR740102: AA polarity
- GRAR740103: AA volume
- ISOY800101: AA normalized relative frequency of alpha-helix
- JANJ780101: AA average accessible surface area
- JOND920101: AA relative frequency of occurrence
- JOND920102: AA relative mutability
- JURD980101: AA modified Kyte-Doolittle hydrophobicity scale
- KLEP840101: AA net charge
- ZIMJ680104: AA isoelectric point
- cnt intsc: sum of 'contact' interaction scores
- cnt nrint: number of 'contact' edges (atomic interactions)
- cnt unweighted: number of 'contact' edges (residue interactions)
- combi intsc: sum of 'combi' interaction scores
- combi nrint: number of 'combi' edges (atomic interactions)
- combi unweighted: number of 'combi' edges (residue interactions)
- hbond intsc: sum of 'hbond' interaction scores
- hbond nrint: number of 'hbond' edges (atomic interactions)
- hbond unweighted: number of 'hbond' edges (residue interactions)
- ovl intsc: sum of 'overlap' interaction scores
- ovl nrint: number of 'overlap' edges (atomic interactions)
- ovl unweighted: number of 'overlap' edges (residue interactions)
- Example
To create a RIN using a job file (as provided in the TEST directory or created for versions of RINalyzer below 0.5), execute the command:
INST_DIR/RINerator_V0.5.X/Source/get_ncint.py Test/JOBS/test_job_*.py
Description of the job files and further instructions can be found here.