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Command-line Options List¶

This page lists the main command-line options available in CABS-flex standalone 3, grouped by function. It is intended as a reference for users who need to check syntax, arguments, or option-specific behavior. For workflow-oriented guidance, see Protein Flexibility, Peptide Modeling, and Peptide–Protein Docking.

1. Input & Initial Structure¶

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-i, --input-protein INPUT¶

Load input protein structure.

INPUT can be either:

• PDB code (optionally with chain IDs) i.e. -i 1CE1:HL loads chains H and L of 1CE1 protein structure downloaded from the PDB database
• PDB file (optionally gzipped)

Note that only protein chain(s) are extracted from the input file, discarding all non-protein molecules.

-c, --config FILE¶

Read options from FILE.

-L, --load-cabs-files FILE¶

Load CABS simulation data file for repeated scoring and analysis of CABS trajectories (with new settings, for example using a reference complex structure and --reference option). Both a path to a file or a path to a directory containing a *.cbs file are valid inputs.

--pdb-cache-dir DIR¶

Set the directory where a subdirectory .cabsPDBcache will be created to store downloaded PDB files (default: ~).

--receptor-ss STR¶

Manually assign secondary structure to the receptor chains.

STR should be either:

• string in the form of: [CHAIN_ID]:[SECONDARY]/[CHAIN_ID]:[SECONDARY] i.e A:CHHHCEEEC+B:CEEEECCCHHHCC
• filename of the text file — one chain per line as in:

A:CHHHCEEEC
B:CEEEECCCHHHCC

-F, --disulfide-bonds RESIDUE1 RESIDUE2¶

Add disulfide bonds to the structure. This option can be used multiple times to add multiple bonds.

Each input should be in the form of exactly one pair: 1:A 14:A. Example: -F 1:A 14:A -F 3:A 13:A appends the disulfide bonds (1:A, 14:A) and (3:A, 13:A). NOTE: Ensure that the residues in each pair are valid and appropriate for disulfide bonding.

--backbone-cyclization CHAIN¶

Indicate if this is a backbone cyclic peptide protein. CABS adds a restraint between the first and last residues of the specified chains. By default, cyclization is added for chain 'A' if no argument is provided.

Examples:

--backbone-cyclization       # Chain A is cyclic
--backbone-cyclization --backbone-cyclization B  # Chains A and B are both cyclic

Invalid:

--backbone-cyclization A B   # Error: only one chain can be specified per use of --backbone-cyclization

2. The Protein Model (Flexibility & Restraints)¶

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For a detailed explanation of restraints and automatic restraint-generation modes, see Restraints and Flexibility Modes.

Global Restraints (Base Model)¶

-g, --protein-restraints MODE [GAP MIN MAX]¶

This options allows to generate a set of binary distance restraints for C-alpha atoms, that keep the protein in predefined conformation.

Note: Default differs between CABSflex (['flexible', 3, 3.8, 11.5]) and CABSdock (['rigid', 5, 5.0, 15.0]). You can provide either a single keyword (the MODE), in which case default parameters associated with that mode and the application will be used, or you can provide all 4 arguments (MODE, GAP, MIN, MAX).

MODE can be either based on plDDT or secondary structure:

• flexible — Generates restraints only for secondary structure elements (helices/sheets). Loops remain free. This is the default.
• plddt — Generates restraints based on AlphaFold pLDDT scores and secondary structure (requires --protein-plddt).
• rigid — Generates restraints for all residues. Results in a stiff model (good for checking local stability).
• ss1 — Restored and natively supported legacy mode. Restrains a residue pair if at least one of the residues belongs to a regular secondary structure element (helix/sheet).
• manual — Requires --protein-category or --protein-flexibility files to define restraint logic.
• none, unleashed, or no-protein-restraints — No protein restraints are generated.

GAP specifies minimal gap along the main chain for two residues to be restrained. MIN and MAX are min and max values in Angstroms for two residues to be restrained.

Note: For users familiar with older versions of CABS-flex, the legacy modes ss2 and all are handled as follows:

• ss2 → Fully supported as a backward-compatible alias. Automatically maps to flexible with a friendly warning in the log.
• all → Fully supported as a backward-compatible alias. Automatically maps to rigid with a friendly warning in the log.

Global Overrides & Modifiers¶

-N, --no-protein-restraints¶

Do not automatically generate any protein restraints. This option has precedence over '--protein-restraints' option and will overwrite any settings set by the latter. With this flag on restraints can still be added with the '--ca-rest-add' or '--ca-rest-file' options.

--protein-restraints-retain PERCENTAGE¶

Reduce the number of protein restraints by indicating the PERCENTAGE of restraints to retain, where PERCENTAGE is a number from (0, 100]. This option reduces the number of automatically generated restraints for the protein molecule to speed up computation. Restraints are randomly removed so that the final number of restraints N_final = N_all * (PERCENTAGE / 100). PERCENTAGE must be greater than 0 and at most 100.

--ca-rest-weight WEIGHT_MIN WEIGHT_MAX¶

Set global weights for all C-alpha restraints (including automatically generated restraints for the protein) when distance is shorter than minimum (WEIGHT_MIN) or longer than maximum (WEIGHT_MAX).

Note: Default differs between CABSflex ([3.5, 0.5]) and CABSdock ([1.0, 1.0]).

--sc-rest-weight WEIGHT_MIN WEIGHT_MAX¶

Set global weight for all SC restraints when distance is shorter than minimum (WEIGHT_MIN) or longer than maximum (WEIGHT_MAX) (default: [1.0, 1.0]).

-b, --binding-interactions FACTOR¶

This option scales the side chains interactions between protein chains by the FACTOR in relation to the side chains interactions within single protein chain. (default: 1.0) i.e. -b 2.0 makes inter-chain interactions two times stronger than intra-chain.

Flexibility (Per-Residue Definition)¶

-f, --protein-flexibility FLEXIBILITY¶

Modify flexibility of selected protein's residues:

• f = 0 — fully flexible backbone
• f = 1 — almost stiff backbone (default: 1.0)
• >1 — increased stiffness

FLEXIBILITY can be either:

• positive real number — all protein residues are assigned the same flexiblity equal that number
• bf — flexibility for each residue is read from the beta factor column of the CA atom in the pdb input file (Note that standard beta factor in pdb file has opposite meaning to CABS flexibillity, edit pdb accordingly or use FLEXIBILITY = 'bfi')
• bfi — flexibility is assigned from the inverted beta factors in the input pdb file so that: bf <= 0.0 -> f = 1.0; bf >= 1.0 -> f = 0.0; f = 1 - bf otherwise.
• bfg — flexibility is assigned from the beta factors in the input pdb file, so that: f = exp(-bf * bf / 2.) and f = 1.0 if bf < 0.0
• <filename> — flexibility is read from file <filename> in the following format:

default <default flexibility value> (if omitted default f = 1.0)
resid_ID <flexibility> i.e. 12:A 0.75 OR resid_ID - resid_ID <flexibility> i.e. 12:A - 15:A  0.75

Multiple entries can be used.

--protein-plddt FLEXIBILITY¶

Read pLLDT values in order to modify flexibility of selected protein's residues:

pLLDT can be either:

• pdb or bf — pLLDT for each residue is read from the beta factor column of the CA atom in the pdb input file.
• <filename> — pLDDT is read from file <filename> and must be either in .json or .tsv format.

--protein-category FLEXIBILITY¶

Modify category of flexibility for selected protein's residues:

• category = 0.0 — highly flexible backbone
• category = 1.0 — medium flexible backbone
• category = 2.0 — lowly flexible backbone
• category = 3.0 — rigid backbone

Category is read from file <filename> in the following format:

default <default category value> (if omitted default will be set according to plddt and secondary structure)
resid_ID <category> i.e. 12:A 2.0 OR resid_ID - resid_ID <category> i.e. 12:A - 15:A  1.0

Multiple entries can be used.

Manual Restraints (Additive/Per-Residue)¶

--ca-rest-add RESI RESJ DIST WEIGHT¶

Add distance restraint between C-alpha (CA) atom in residue RESI and C-alpha atom in residue RESJ. DIST is a distance between these atoms and WEIGHT is restraint's weight (number from [0, 1]). In order to add restraints between the peptide and the protein, or between two peptides, use PEP1, PEP2, ... as chain identifiers of the peptides (even when peptide is read from a pdb file its chain identifier is ignored). i.e. --ca-rest-add 123:A 5:PEP1 8.7 1.0 adds restraint between the C-alpha atom of the residue number 123 in the chain A of the protein and the C-alpha atom of the 5th residue of the peptide. If you add only one peptide both 'PEP' and 'PEP1' is a valid chain identifier. If you add multiple peptides they will be ordered as follows:

1. from config file added by the 'peptide' option
2. from config file added by the 'add-peptide' option
3. from command line added by the '-p, --peptide' option
4. from command line added by the '--add-peptide' option.

Peptides added by the same method preserve the order by which they appear in the config file, or on the command line. Option can be used multiple times to add multiple restraints.

A chain identifier is required even for single-chain proteins.

Command example:

CABSflex -i 4PTI -a 10 -y 20 --ca-rest-add 5:A 15:A 8.7 1.0

--ca-rest-file FILE¶

Read C-alpha restraints from file (use multiple times to add multiple files).

--sc-rest-add RESI RESJ DIST WEIGHT¶

Add distance restraint between SC pseudoatom in residue RESI and SC pseudoatom in residue RESJ. For more details see help for --ca-rest-add

--sc-rest-file FILE¶

Read SC restraints from file (use multiple times to add multiple files).

3. Simulation Parameters¶

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For a detailed explanation of CABS Monte Carlo steps, cycles, replicas, reduced temperatures, and simulated annealing, see Sampling and Temperature.

Temperature¶

-t, --temperature TINIT TFINAL¶

Set temperature range for simulated annealing. TINIT — initial temperature, TFINAL — final temperature. CABS uses temperature units, which do not correspond straightforwardly to real temperatures. Temperature around 1.0 roughly corresponds to nearly frozen conformation, folding temperature of a small proteins in the CABS model is usually around 2.0.

Note: Default differs between CABSflex ([1.4, 1.4]) and CABSdock ([2.0, 1.0]).

Sampling Control¶

-y, --mc-cycles NUM¶

Set number of Monte Carlo cycles to NUM (NUM>0, default: 50). Total number of snapshots generated for each replica/trajectory = [mc-annealing] x [mc-cycles], (default: 20 x 50 = 1000).

-s, --mc-steps NUM¶

Set number of Monte Carlo cycles between trajectory frames to NUM (NUM > 0, default: 50). NUM = 1 means that every generated conformation will occur in trajectory. This option enables to increase the simulation length (between printed snapshots) and doesn't impact the number of snapshots in trajectories (see also --mc-cycles description).

-a, --mc-annealing NUM¶

Set number of Monte Carlo temperature annealing cycles to NUM (NUM > 0, default: 20).

--disable-centro¶

Disable centrosymmetric potential in the simulation. (default: False)

-z, --random-seed SEED¶

Set seed for random number generator.

Replica Exchange¶

-r, --replicas NUM¶

Set number of replicas to be used in Replica Exchange Monte Carlo.

Note: Default differs between CABSflex (1) and CABSdock (10).

-D, --replicas-dtemp DELTA¶

Set temperature increment between replicas. (DELTA > 0, default: 0.5).

4. CABSdock (Peptide Docking)¶

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Peptide Input¶

-p, --peptide PEPTIDE¶

(CABSdock only) Load peptide sequence and optionally peptide secondary structure in one-letter code. Can be used multiple times to add multiple peptides.

PEPTIDE can be either:

• amino acid sequence in one-letter code (optionally annotated with secondary structure: H — helix, E — sheet, C — coil) i.e. -p HKILHRLLQD:CHHHHHHHHC loads HKILHRLLQD peptide with secondary structure CHHHHHHHHC
• PDB code (optionally with chain ID) i.e. -p 1CE1:P loads the sequence of chain P from 1CE1
• PDB file with peptide's coordinates — loads only peptide sequence from the PDB file

Hint: If possible, it is always recommended to use secondary structure information/prediction. For residues with ambiguous secondary structure prediction assignment it is better to assign coil (C) than the regular (H — helix or E — extended) type of structure.

--peptide PEPTIDE is an alias for --add-peptide PEPTIDE random random.

-P, --add-peptide PEPTIDE CONFORMATION LOCATION¶

(CABSdock only) Add peptide to the complex. This option can be used multiple times to add multiple peptides.

PEPTIDE must be either:

• amino acid sequence in one-letter code (optionally annotated with secondary structure: H — helix, E — sheet, C — coil) i.e. -P HKILHRLLQD:CHHHHHHHHC random random loads HKILHRLLQD peptide with secondary structure CHHHHHHHHC
• PDB file (may be gzipped)
• PDB code (optionally with chain_id i.e. 1abc:D)

Hint: If possible, it is always recommended to use secondary structure information/prediction. For residues with ambiguous secondary structure prediction assignment it is better to assign coil (C) than the regular (H — helix or E — extended) type of structure.

CONFORMATION sets initial conformation of the peptide:

• random — random conformation is generated
• keep — preserve conformation from file (no effect if PEPTIDE=SEQUENCE)

LOCATION sets initial location for the peptide:

• random — peptide is placed in a random location on the surface of a sphere centered at the protein's geometrical center at distance defined by --separation from the surface of the protein
• keep — preserve location from file (no effect if PEPTIDE=SEQUENCE)
• PATCH — list of protein's residues (i.e 123:A+125:A+17:B). Peptide will be placed above the geometrical center of listed residues at distance defined by --separation from the surface of the protein

Warning: Residues listed in PATCH should be on the surface of the protein and close to each other.

--peptide-structure-prediction¶

Treat input as a string 'SEQUENCE' or 'SEQUENCE:SECONDARY' for peptide structure prediction.

--nsp3-model-path PATH¶

Path to the NetSurfP-3.0 model weights. Providing this path allows CABS to predict the secondary structure of peptides when it is not included in the input. Ensure that NetSurfP-3.0 is installed and provide the path to its model weights file here. If NetSurfP-3.0 is not installed or the path is not provided, peptides will default to a secondary structure consisting only of coil (C).

--align-peptide-options KEY=VAL [KEY=VAL ...]¶

Path to alignment with reference structure. If set, the '--align' option is ignored.

Docking Search¶

-d, --separation DISTANCE¶

(CABSdock only) This option enables advanced settings of building starting conformations of modelled complexes. The option sets separation distance in Angstroms between the peptide and the surface of the protein. (default: 20.0 Angstroms)

--insertion-attempts NUM¶

(CABSdock only) This option enables advanced settings of building starting conformations of modelled complexes. The option sets number of attempts to insert peptide while building initial complex (default: 1000).

--insertion-clash DIST¶

(CABSdock only) This option enables advanced settings of building starting conformations of modelled complexes. The option sets distance in Angstroms between any two atoms (of different modeled chains) at which a clash occurs while building initial complex (default: 1.0 Angstrom).

--pairmod FILENAME¶

(CABSdock only) Read from file weights and shifts for pairwise potential between the receptor and selected peptide residues.

One line per one peptide residue in the following format:

res_id weight shift

Example:

3:PEP1 1.25 0.75
5:PEP1 1.50 0.50

-e, --exclude RESIDUES¶

(CABSdock only) Exclude protein residues listed in RESIDUES from the docking search. This enforces more effective search in other areas of the protein surface. For example, it may be known that some parts of the protein are not accessible to the peptide (due to binding to other proteins) and therefore it could be useful to exclude these regions from the search procedure.

RESIDUES must be a single string of characters (no whitespaces) consisting of residue identifiers (i.e. 123:A) or chain identifiers (i.e. A) joined with the + sign. - is also allowed to specify a continuous range of residues or chains.

Examples:

-e 123:A              # excludes residue 123 from chain A
-e 123:A+125:A        # residues 123 and 125 from chain A
-e 123:A-125:A        # residues 123, 124 and 125 from chain A
-e A                  # whole chain A
-e A+C                # chains A and C
-e A-C                # chains A, B and C

Adding @PEP<N> at the end of the string limits the excluding to only the N-th peptide. i.e. -e 123:A@PEP1 will exclude residue 123 in chain A for binding with the first peptide only. If @PEP<N> is omitted the exclusion list affects all peptides.

This option can be used multiple times to add multiple sets of excluded residues.

--excluding-distance DIST¶

(CABSdock only) Set minimum distance between side chain atoms of peptide(s) and protein residues marked as 'excluded'. (default: 5.0)

5. Analysis & Alignment¶

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Reference & Alignment¶

-R, --reference-pdb REF¶

Load reference complex structure. This option allows for comparison with the reference complex structure and triggers additional analysis features.

REF must be either:

• [pdb code]:[protein chains]:[peptide1 chain][peptide2 chain]...
• [pdb file]:[protein chains]:[peptide1 chain][peptide2 chain]...

i.e 1abc:AB:C, 1abc:AB:CD, myfile.pdb:AB:C, myfile.pdb.gz:AB:CDE

--align METHOD¶

Select the method to be used to align target with reference pdb.

Available options are: (default SW)

• SW — Smith-Waterman
• blastp — protein BLAST (requires NCBI+ package installed)
• trivial — simple sequential alignment, useful only to speed up run (by omitting Smith-Waterman algorithm) in case of obvious one-chain input and reference of the same length (e.g. when input and reference are the same file).
• CSV — loads alignment from given file (passed as alignment setting called fname) in format described by Berbalk et. al. in 2009.

--align-options KEY=VAL [KEY=VAL ...]¶

Path to alignment with reference structure. If set, the '--align' option is ignored. Example:

--align blastp --align-options task=short-task

--peptide-rmsd-mode MODE¶

Select peptide RMSD comparison policy. (default: auto)

Available options are:

• strict — require full peptide alignment
• overlap — allow strict first, then use only exactly aligned overlapping residues
• mutational — allow strict and overlap first, then use mismatch-tolerant local alignment
• auto — alias for mutational

--peptide-min-aligned-length NUM¶

Minimum number of peptide residues that must be aligned for overlap or mutational peptide RMSD modes. (default: 5)

--peptide-min-aligned-fraction FRAC¶

Minimum fraction of the shorter peptide that must be aligned for overlap or mutational peptide RMSD modes. (default: 0.5)

--peptide-min-identity FRAC¶

Minimum sequence identity over aligned peptide positions required for mutational peptide RMSD mode. (default: 0.5)

--peptide-max-gap-fraction FRAC¶

Maximum allowed gap fraction in mutational peptide RMSD mode. (default: 0.4)

--peptide-min-contiguous-block NUM¶

Minimum length of the longest contiguous peptide alignment block required for overlap or mutational peptide RMSD modes. (default: 3)

--weighted-fit ARG¶

This option allows to set and customize the way models are structurally aligned, which affects both calculation of the RMSD/RMSF and clustering together with the selectiom of the final models. Models are aligned by the Kabsch optimal fit algorithm. This options assigns weights to all atoms, which specify how 'important' the atom is in the structural fit process. Weights are numbers from [0:1] range with '0' meaning 'irrelevant in fitting process.'

ARG can be either:

• gauss — Weights are generated automatically in the iterative procedure described in Biophys J. 2006 Jun 15; 90(12): 4558-4573. The procedure consists of the following steps: (1) Set wi = 1.0 for i = [1,2 ... N], where N is the number of atoms. (2) Align structures using weights wi. (3) Calculate di - displacement of the i-th atom. (4) Update weights according to formula: wi = exp(-0.5 * di * di). Repeat (2) through (4) until convergence.
• flex — Weights are taken from the flexibility settings. (See help entry for --protein-flexibility)
• ss — Weights are taken from the secondary structure assignment. Atoms in helices and sheets are given w = 1.0, while those in loops and coil get w = 0.0
• <filename> — Weights are read from a file <filename>. The file should follow this format:

# Example file
# default 1.0 (default value, if omitted w = 1.0 is assumed)
# 1:A 0.5
# 5:A 0.1
# ...
# 1:B 0.99
# ...
# End of file

• off — Turns off weighted-fit (all weights are 1.0).

Note: Default differs between CABSflex (gauss) and CABSdock (off).

--gauss-iterations NUM¶

Sets number of iterations of dynamic weighted-fit algorithm used for superposition of structures. This option has no effect when --weighted-fit is set to anything other than 'gauss'. NUM = 100 by default.

Clustering & Filtering¶

-k, --clustering-medoids NUM¶

Set number of medoids in k-medoids clustering algorithm. This option also sets number of final models to be generated. (default: 10).

--clustering-iterations NUM¶

Set number of iterations of the k-medoids clustering algorithm. (default: 100).

-n, --filtering-count NUM¶

Set number of low-energy models from trajectories to be clustered (default 1000).

--filtering-mode MODE¶

Choose the filtering mode to select NUM (set by '--filtering-count') models for clustering.

MODE can be either: (default: each)

• each — models are ordered by protein-peptide(s) binding energy and top n = [NUM / R] (R is the number of replicas) is selected from EACH replica
• all — models are ordered by protein-peptide(s) binding energy and top NUM is selected from ALL replicas combined

Contact Maps¶

-M, --contact-maps¶

Store contact maps matrix plots and histograms of contact frequencies. (default: False).

-T, --contact-threshold DIST¶

Set contact distance between side chains pseudoatoms (SC) for contact map plotting. (default: 6.5).

--contact-threshold-aa DIST¶

Set contact distance between heavy atoms for contact map plotting. (default: 5.5).

--contact-map-colors CLR1 CLR2 ... CLR6¶

Sets 6 colors (hex code, e.g. #00FF00 for green etc.) to be used in contact map color bars. (default: ['#ffffff', '#f2d600', '#4b8f24', '#666666', '#e80915', '#000000']).

Command example:

CABSflex -i 1CE1 -a 10 -y 20 --contact-map-colors  ['#ff0fff', '#f2d610', '#4b9f24', '#666366', '#e80215', '#000100']

6. Reconstruction (All-Atom)¶

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For a detailed explanation of deep-learning-based (cg2all) and spatial-restraints-based (Modeller) all-atom reconstruction pipelines, see All-Atom Reconstruction.

-A, --aa-rebuild [MODE]¶

Rebuild models to all-atom representation. Supported modes:

• M — rebuild Medoids (model_?.pdb) sequentially (default)
• C — rebuild Clusters (cluster_?.pdb) in parallel
• T — rebuild Trajectories (replica_?.pdb) in batch DCD
• A — rebuild ALL of the above

--aa-method ARG¶

Set method for all-atom reconstruction.

ARG can be either:

• cg2all — use cg2all package for all-atom reconstruction (default)
• modeller — use MODELLER package for all-atom reconstruction

--cg2all-representation REP¶

Coarse-grained representation passed to cg2all when --aa-method cg2all is used. REP can be either calpha for CA-only reconstruction or calpha-sc for CA plus CABS side-chain pseudoatoms. (default: calpha-sc)

--aa-minimize [BOOL]¶

Enable vacuum energy minimization of reconstructed all-atom structures using the OpenMM simulation framework.

• When set to True (or --aa-minimize without value), all-atom structures undergo a 500-iteration vacuum energy minimization with the modern Amber19 forcefield (amber19-all.xml featuring improved ff19SB backbone/CMAP correction parameters).
• By default, single-model medoids (model_?.pdb) are minimized automatically to eliminate severe steric clashes (typically reducing Phenix/MolProbity clashscores from >200 down to ~1–5), whereas multi-model trajectories/replica ensembles are minimized only if explicitly requested by the user.
• To completely disable minimization for all outputs, pass --aa-minimize false.

-m, --modeller-iterations NUM¶

Set number of iterations for reconstruction procedure in MODELLER package (default: 3). Bigger numbers may result in more accurate models, but reconstruction takes longer.

--cg2all-env-prefix DIR¶

Path to the isolated environment containing cg2all dependencies. Required if --aa-method cg2all is used.

7. Output Control¶

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File Saving¶

-S, --save-cabs-files¶

Save CABS simulation file. The filename will have the following format: %yy%mm%dd%HH%MM%SS%RANDOMSTRING.cbs. For example: 181116161924knWPtn.cbs

-C, --save-config¶

Save simulation parameters in config file.

--generate-chimera-visualizations¶

Generate ChimeraX script files (.cxc) to easily view simulations, models, and contact maps. For details, see Visualization Guide.

--generate-pymol-visualizations¶

Generate PyMOL script files (.pml) to easily view simulations, models, and contact maps. For details, see Visualization Guide.

--generate-notebook¶

Generates a Jupyter Notebook (report.ipynb) and an HTML report (report.html) with interactive visualization and analysis outputs. For details and screenshots, see Report Notebook.

PDB Output¶

-o, --pdb-output SELECTION¶

Select structures to be saved in the pdb format.

Available options are:

• A — all (default)
• R — replicas
• F — filtered
• C — clusters
• M — models
• S — starting
• N — none

i. e. -o RM — saves replicas and models.

Automated Visualization¶

--generate-pymol-visualizations¶

Force-enable output flags needed to visualize the results, and generate PyMOL script files (.pml) to easily view simulations, models, and contact maps. For details, see Visualization Guide.

--generate-chimera-visualizations¶

Force-enable output flags needed to visualize the results, and generate ChimeraX script files (.cxc) to easily view simulations, models, and contact maps. For details, see Visualization Guide.

--generate-notebook¶

Generates a Jupyter Notebook (report.ipynb) and an HTML report (report.html) with interactive visualization and analysis outputs. For details and screenshots, see Report Notebook.

Data Formatting¶

--renumber-residues-to-original¶

Renumber residues in output PDB files to match the original residue numbering from the input structure. (default: False)

--pdb-bfac-output SELECTION¶

Select what values should be saved in beta factors of the initial PDB structure.

Available options are:

• A — all
• B — original beta factors of CA
• C — flexibility categories
• P — pLDDTs
• R — RMSFs
• S — secondary structure
• N — none (default)

i. e. --pdb-bfac-output BP — saves original beta-factors and pLDDTs.

--csv-output SELECTION¶

Select what values should be saved in csv format.

Available options are:

• A — all
• B — original beta factors of CA
• C — flexibility categories
• P — pLDDTs
• S — secondary structure
• N — none (default)

i. e. --csv-output BP — saves original beta-factors and pLDDTs.

--json-output¶

Enable JSON format output for analysis results. (default: False)

--dssp-output¶

Save DSSP secondary structure analysis to a file. (default: False)

--ss-output¶

Save secondary structure assignments to a file. (default: False)

--restraints-output¶

Save generated restraints to a file. (default: False)

--disable-side-chain-centers [BOOL]¶

Disable writing side chain centers in the output PDB files (default: None).

--write-sc-start-pdbs [BOOL]¶

Enables writing side chain starting PDB files. (default: False)

--image-file-format FMT¶

Save all of the image files in given format. (default: svg).

Logging¶

-v, --verbose LEVEL¶

Set verbosity LEVEL: (default: 2)

• 0 — silent mode (only CRITICAL messages)
• 1 — WARNINGS
• 2 — INFO
• 3 — LOG FILES (log files are generated)
• 4 — DEBUG (all messages)

--log¶

Automatically redirects output to a CABS.log file created in the working directory and stops progress bar from showing on higher verbosity levels and turns off log coloring. Piping standard error will not work with this option. If a log file already exists it will be appended to.

--no-progress-bar¶

Disables the progress bar.

8. System & Tools¶

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-w, --work-dir DIR¶

Set working directory to DIR. (default: .)

--fortran-command PATH¶

Provide path to fortran compiler binary (default is 'gfortran -O2').

--version¶

Print version and exit program.

-h, --help¶

Print help and exit program.

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