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Options and Parameters
Here you can find more information on parameters and options available on the command line, in the graphical user interface and on the web service.
At least one of these is required for execution on the command line.
Pore ID [pore-id]: Identifies all pores in a given protein PDB file, and for each pore generates a tab-separated file with lining residues and a pseudo PDB file with the empty space within the pore. The pseudo PDB file can be used for visualising the pore together with the protein.
Axis Trace [axis-trace]: Determines the axis of a pore or cavity and writes it into a pseudo PDB file for visualisation. Some pores have multiple axes, in which cases several output files are generated.
Gate Opening [gate-open]: Rotates the shared lining residues of two neighbouring pores in an effort to open the gate between them as much as possible. The result is a PDB file of the entire protein with the rotated residues.
PDB input file [-i <path>]: Required file with protein information such as IDs, names and coordinates of atoms and residues in Protein Data Bank (.pdb) format.
Result directory [-o <path>]: Directory that is going to contain a sub-directory of the current ProPores2 run. Output files can include files for identified pores (pseudo-PDB), their axes (pseudo-PDB) and lining residues (tab-separated), as well as versions of the input protein (PDB) withopen gates between neighbouring pores. If the sub-directory already exists and pore-ID is run, its content will get deleted!
PDB and pseudo-PDB files can be visualised with PDB-viewers such as Chimera or PyMOL.
Help [-h, --help]: Show the help message with parameters and options on the command line.
Result name [--name <string>]: Name of the result sub-directory as well as prefix of all output files. If the field is left blank, the name of the input protein PDB file is automatically used. Example: If the input PDB file is "example_data/1EA5.pdb", then this defaults to "1EA5". If the result directory is "results/", all results will be written to "results/1EA5/".
Hydrogen processing [--h-atom <number>]: This setting allows to fine-tune how hydrogen atoms should be dealt with when reading in the input protein file, and can distinguish between hydrogen atoms in PDB protein atom records (ATOM) and hydrogen atoms in non-protein atom records (HETATM). The options are:
0: keep all H atoms
1: remove all H atoms
2: remove only H atoms in ATOM records
3: remove only H atoms in HETATM records
The default behaviour is to keep all hydrogen atoms.
Hetero atom processing [--hetero <number>]: Hetero atoms are non-protein atoms listed under "HETATM" in a PDB file. Some PDB files also contain dummy atoms as HETATM records, for example membrane dummy atoms in PDBs from the OPM database. This settings can be used to specify how hetero atoms should be dealt with when reading in the input protein file. The options are:
0: keep all hetero atoms
1: remove all hetero atoms
2: remove all hetero atoms except dummy atoms
3: remove only dummy hetero atoms
The default behaviour is to keep all hetero atoms.
Keep alternative locations [--keep-alternative]: Some atoms have multiple possible locations in the input protein file. By default, only the primary location is considered and the other locations are ignored. If enabled, all locations will be kept, which means that all alternative locations will be loaded as additional atoms. By default this is disabled.
Skip non-standard amino acids [--skip-non-std-amino-acids]: Protein atoms are listed under "ATOM" in a PDB file. If enabled, all "ATOM" records with not standard residue names (ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAl) will be ignored when loading the PDB file. Atoms in "HETATM" records are not affected by this. By default this is disabled.
Resolution [-b <decimal>]: Pore ID places the protein on a 3D grid. The resolution specifies the length of a single grid box. The smaller the resolution value, the more fine-grained the computed pores, but also the potentially longer the required runtime. The unit is Ångström and the default value is 1.0 Å.
Solvent radius [-s <decimal>]: To identify pores on the surface, Pore ID checks if enclosed areas in the protein are accessible for the surrounding solvent, i.e. water molecules with a radius of 1.4 Å. If the value is increased, hollow areas in the protein must also be accessible for these larger molecules to be classified as pores and not cavities. The unit is Ångström and the default value is 1.2 Å.
Probe radius [-p <decimal>]: After the solvent accessible surface (SAS) of the protein is computed (see above), Pore ID "rolls" a probe across this surface and removes shallow surface regions that are not deeper than the probe. The higher this value, the deeper surface areas need to be before they are considered to be part of a pore. The unit is Ångström and the default value is 1.4 Å.
Volume threshold [-v <decimal>]: Minimum volume (size) of pores and cavities. Smaller potential pores and cavities are not included in the results or further analysis steps. The unit is cubic Angstrom and the default value is 50 ų.
Computation mode [--mode <number>]: Enclosed spaces within the protein or on its surface can be computed in several ways. By default, Pore ID tries to guess the most efficient version for each run (autodetect).
0: autodetect
1: ray trace, faster for smaller proteins or higher resolution values; increased RAM usage
2: standalone, potentially faster for larger proteins or lower resolution values; reduced RAM usage
Pore type [--pore-filter <number>]: By default, Pore ID generates results for pores and cavities. This can be restricted to only pores (accessible from the protein surface) or to only cavities (completely enclosed by the protein). The options are:
0: pores and cavities
1: only pores
2: only cavities
The default behaviour is to output all types of pores.
Preparation [--preparation <number>]: By default, Pore ID prepares files for gate open or axis trace when they are not currently enabled so that they can be run at a later point without having to re-run Pore ID. This behaviour can be controlled with this option. The options are:
0: axis-trace and gate-open
1: only axis-trace
2: only gate-open
3: no preparation
The default behaviour is to output files for axis trace and gate open.
Surface patch threshold [-spt <number>]: Minimum area of a pore surface patch in for it to count as a potential pore axis origin. The unit is square Ångstrom and the default value is 30 Ų.
Single input file [-ts <path>]: Path to a single axis trace input file from a previous Pore ID run with enabled "axis trace preparation". Only needed if axis trace is not run together with pore ID.
Input directory [-td <path>]: Path to a directory with one or more axis trace input files from a previous Pore ID run with enabled "axis trace preparation". Only needed if axis trace is not run together with pore ID.
Clash tolerance [-ct <decimal>]: Van der Waals radius overlap tolerance (clash tolerance) for rotamer generation in Ångstrom. Lowering the clash tolerance can substantially speed up the gate-open runtime, but too low values can also eliminate all potential rotamers. The default value is 0.75 Å.
Single input file [-gs <path>]: Path to a single gate open input file from a previous Pore ID run with enabled "gate opening preparation".Only needed if gate-open is not run together with pore ID.
Input directory [-gd <path>]: Path to a directory with one or more gate open input files from a previous Pore ID run with enabled "gate opening preparation". Only needed if gate-open is not run together with pore ID.
Rotamer library [--rotamers <path>]: Running gate opening requires a library of viable rotamer conformations for each standard amino acid. ProPores2 comes with a rotamer library that it will try to automatically load. This settings can be used to set the path manually, in case the library was saved in a different location or was renamed, or ProPores2 is unable to find it for other reasons.
Gate difficulty [--difficulty <number>]: Some amino acids only have a small number of possible rotamers, while others have over 10,000. Depending on the number of residues in the gate and the number of possible rotamers of each gate residue, opening the gate can be very fast or take a long time. This setting allows to skip gates that are likely to take a long time to compute.
0: try to open all gates
1: skip very time intensive gates
2: skip potentially time intensive gates
The default behaviour is to try opening all gates.
Re-estimate difficulty [--re-estimate]: If enabled, the estimated difficulty of potential gates is re-assessed after all rotamers have been generated and clashes with the rest of the protein have been eliminated, thus leaving a potentially much reduced number of possible rotamer combinations. By default this is disabled.