Secondary Structure Determination

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 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 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.

ss-hx-range

Analyze an existing *.ss file, outputting the residue ranges defining helices, one per line.

usage:
ss-hx-range your.ss output.range

ss-sheet-range

Analyze an existing *.ss file, outputting the residue ranges defining strands in sheets, one per line.

usage:
ss-sheet-range your.ss output.range

ahelix

Used by pdb-geom-ss .

See $RIBBONS_HOME/fithx/ for scripts and examples.

turn-class

Analyze the output of pdb-rama-ss to classify turns based on phi/psi angles.

usage:
turn-class < your.rama > output

O-xxx-ss
X-xxx-ss

This has been superceded by the ribbons-error analysis.
Modify an existing *.ss file, adding a column for coloring based on output of X-PLOR or O. See $RIBBONS_HOME/analysis/xplor/ or $RIBBONS_HOME/analysis/O/ for scripts and examples.


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