Secondary Structure Determination

pdb-pro-ss --- make protein *.ss file from H-bonding patterns
pdb-rama-ss --- make or add to protein *.ss file from phi/psi
pdb-range-ss --- add to *.ss file, color by residue ranges
pdb-nuc-ss --- make nucleic acid *.ss file
pdb-bf-ss --- add to *.ss file, color by residue B-factors
turn-class --- analyzes classes of beta-turns
ss-hx-range --- determine residue ranges of helices from *.ss file
ss-sheet-range --- determine residue ranges of sheets from *.ss file
ahelix --- analyze secondary structure from C-alpha only
pdb-chis-ss --- add to protein *.ss file from sidechain dihedrals
pdb-geom-ss --- make or add to protein *.ss file from differential geometry

All ribbons must have a *.pdb and an associated *.ss file. Programs exist to automatically generate a sensible *.ss files for proteins --- in practice the user will make modifications according to experience. The nucleic acids are all given a value of ``sheet'' for best results. Other programs ``edit'' the default *.ss files, adding columns for additional color-coding information. The user is encouraged to add extra columns for custom results.

The programs all have the following general usage features:

usage:
pdb-xxx-ss molecule.pdb molecule.ss [< input] > output

errors:
*.pdb file does not exist.
*.ss file already exists.

pdb-pro-ss

Create a *.ss file for a single protein chain. Determine the secondary structure from hydrogen bonding patterns. An implementation of the Kabsch & Sander algorithm has been coded.

usage:
pdb-pro-ss molecule.pdb molecule.ss < input > output

queries:
Enter a title for output ribbon SS file:

The output *.ss file has columns for sequence, secondary structure, and hydrogen bonding. The ``hb'' column for each residue adheres to the following codes: `B' if both carbonyl and amide form mainchain H-bonds for the residue, `O' carbonyl is not bonded, `H' amide is not bonded, `x' neither are bonded, `P' proline with carbonyl bonded, `Q' is proline with free carbonyl.

Note: the diagnostic output is the summary in Kabsch & Sander notation.

pdb-nuc-ss

Create a *.ss file for a single nucleic acid chain. This is essentially a dummy program. It simply outputs the 1-letter-code for the nucleotide and assigns each residue to a sheet. Suggestions are welcome from nucleic acid specialists.

usage:
pdb-nuc-ss molecule.pdb molecule.ss < input > output

queries:
Enter a title for output ribbon SS file:

pdb-rama-ss

Create a new or modify an existing *.ss file, adding columns for coloring based on phi/psi and omega values of the mainchain torsion angles.

usage:
pdb-rama-ss mol.pdb mol-new.ss < input > output
pdb-rama-ss mol.pdb mol-old.ss > output

queries:
Enter a title for output SS file:

The output *.ss file has additional columns for ``rama'' and ``om''. The ``rama'' maps the phi/psi angles to the letters as shown on the printed version of the plot in the diagnostic output. For example, `E' is highly probable extended conformation, `e' slightly less probable, and `R' is right-handed helical conformation. The grid was determined by a database analysis. The ``om'' gives the omega angle, with `T' for trans, `s' and `u' for slightly below and above 180 degrees, `C' for cis, `b' and `d' near cis, and `X' a bad value.

Note: The diagnostic output can be saved to view as a Ramachandran plot with the command ``rama-plot''. If the latter usage is chosen, the ``mol-old.ss'' will be replaced with its updated version.

pdb-geom-ss

Create a new *.ss file, assigning secondary structure from differential geometry. Only alpha carbons coordinates are used. An implementation of the Louie and Somorjai algorithm has been implemented.

usage:
pdb-geom-ss mol.pdb mol-new.ss > output

The standard `ss' codes are output.

pdb-chis-ss

Modify an existing *.ss file, adding a column for coloring based on the sensibility of the side chain dihedral values. The rotamer dictionary of Ponder and Richards as well as my database analysis have been used.

usage:
pdb-chi-ss mol.pdb mol-old.ss > output

The output *.ss file has additional columns for ``chi''. `N' is for residues with no side chains, `X' for residues with non-standard chi values, `A' is the most probable conformation for that residue, `B' the second best, etc.

pdb-range-ss

Modify an existing *.ss file, adding a column for coloring based on residue ranges. Behaves like ``pdb-range-sph'' (can use same input file).

usage:
pdb-range-ss mol.pdb old.ss [KeyString] > output

queries:
Enter inclusive integer residue range and color index:
Enter another range and color? (EOF to quit)

Note: Default KeyString is `range'. Any range not explicitly set defaults to colorindex 7 (white). To change this, first input a ``range'' consisting of the entire chain, then individually color the various ranges of interest.

pdb-bf-ss

Modify an existing *.ss file, adding a column for coloring based on residue temperature factors.

usage:
pdb-bf-ss old.ss new.ss [KeyString] < input > output

Note: Default color mapping based on database analysis. Average B for proteins is 24, standard deviation is 12.