Secondary Structure Determination.

pdb-sss --- make default *.ss file, plus the most popular options below
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-chi-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-sss

Is a convience script that executes the most common commands below in sequence to create a *.ss file.
1) Runs either 'pdb-pro-ss' or 'pdb-nuc-ss' for default values.
2) Runs 'pdb-rama-ss' to add information on phi/psi values.
3) Runs 'pdb-chis-ss' to add information on sidechain rotamer values.
4) Runs 'pdb-bf-ss' to add information on temperature factors.

It's usage is simpler:

usage:
pdb-sss molecule.pdb

It will create 'molecule.ss', plus assorted data files 'molecule.*'

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, hydrogen bonding, sheets, and N-C run.
The ''ss'' column determines how each residue is to be displayed (you may wish to edit this by hand for prettyness). The ''sshb'' is the original ''ss'' from the algoritm. The special 'X' code indicates a break in the chain between the two residues.
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. The ''sheet'' column groups strands into sheets, as in the the diagnostic output is the summary in the Kabsch & Sander notation. Alpha helices are labeled 'a' and coil 'c'.
The ''run'' breaks the chain into 7 segments, labeled A..G, from the N- to the C- terminus.

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 coded.

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

The standard 'ss' codes are output.

pdb-chi-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 usually use same input file).

usage:
pdb-range-ss mol.pdb old.ss [KeyString [Kol0] ] > output

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

Note: Default KeyString is 'range'. Characters 1..9 by default map to the colorindices 1..9. Characters A..G map a rainbow from blue to red. Any range not explicitly set defaults to colorindex Kol0, which is initially = 7 (white). The ranges can overlap, with later input overwriting the earlier. Eg, first input a large ''range'' consisting of most of the chain, then individually color the various ranges of interest.

Note: When running interactively, CTRL-D gives an EOF signal. It is often convenient to store the input in a file with one range pair and character index per line.

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.

Ribbons User Manual / UAB-CBSE / carson@uab.edu