Tools making use of BiopLib
See INSTALL.md for installation instructions!
Calculates contacts between chains at the atom and residue level. You can get all contacts or contacts between specified chains.
Start of a program for performing various checks on a PDB file
Rewrites the output from naccess solvent accessibility as a standard PDB format file with accessibility in the B-val column and radius in the occupancy column.
Converts a PDB file to input for the Connoly MS program
Converts a PDB file to PDBML format
Converts a PDBML file to PDB format
Extracts a PIR sequence file from a PDB file.
Convert PDB format to GROMOS XYZ. N.B. Does NOT correct atom order.
Counts the number of atoms within the specified radius of each atom in a PDB structure.
Extracts only the coordinates (i.e. ATOM and HETATM records) from a PDB file, discarding the header and footer records
Selects specfied atom types from a PDB file. Assumes C-alpha if no atoms are specified.
Calculates means and standard deviations for B-values per residue.
Calculates an RMS between 2 PDB files. No fitting is performed.
Identifies the residue closest to the centroid of a protein.
Splits a PDB file into chains using distance criteria.
Checks whether a specified residue exists in a PDB file.
Builds CONECT records for a PDB file. Deletes existing records.
Counts chains, residues & atoms in a PDB file.
Rename C-terminal oxygens in standard style and generate second one if required.
Removes atoms from a PDB file which have NULL coordinates (i.e. x = y = z = 9999.0)
Takes one or more zones in a PDB file and outputs all residues of a specified type within a given distance of the zone(s).
Takes a PDB file as input and given a key residue and a number of residues will return the residue identifiers for residues this number of positions before and width after the key residue.
pdbflip is a rather crude and simple program for correcting the atom naming of equivalent atoms about freely rotable bonds.
pdbgetchain reads a PDB file and write out only those chains specified on the command line.
Takes a list of residue specifications and extracts just those residues from a PDB file
Extracts a specified zone from a PDB file
Add hydrogens to a PDB file.
Prints the key header information from a PDB (title; molecule and species for each chain, etc.)
Removes het atoms from a PDB file.
Patches the residue hydrophobicity values into the B-value (temperature factor) column to allow colouring by hydrophobicity.
Removes hydrogens from a PDB file.
Calculates the best fit line through a set of PDB coordinates.
Calculates and lists the disulphides in a PDB file.
Generates a patch around a specified residue.
Correct atom order of a PDB file.
Moves a set of PDB coordinates to the origin.
Takes a patch file containing residue specifications and values one to a line and patches the B-value (or occupancy) for that residue with the specified values.
Patches the numbering of a PDB file from a patch file containing residue numbers.
Renumber a PDB file
Rotates a PDB file
Calculate secondary structure for a PDB file
Allows the extraction of different occupancies and different models from a PDB file
Performs solvent accessibility calculations according to the method of Lee and Richards.
pdbsphere identifies residues within a specified radius of a specified residue.
Split a PDB file into separate files for each chain
Sums the b-values over each residue and places the summed values in the b-value column. Can also calculate averages.
Applies non-cystollographic symmetry operations specified in REMARK 350 records to a PDB file. Note that this program has certain limitations. Run pdbsymm -h for details.
Generates a set of backbone torsions from a PDB file.
Translates a PDB file
Performs a contact analysis at the residue level to find residues whose sidechains contact any atom of the residues specified in a given range
A program similar to (and which predates) Will Valdar's scorecons program for scoring conservation in a sequence alignment.
Applies a standard numbering scheme to a set of PDB files.