CYANA Command: structures secondary

Parameters

structures=integer

(default: 1)

mode=classic|normal|psipred|simple|ovw|sep

(default: normal)

Description

Computes the secondary structure using the DSSP algorithm (Kabsch & Sander, 1983), which is based exclusively on the detection of hydrogen bonds. If multiple structures are selected, the secondary structure is reported for the individual structures only if information level is set to full or higher. Otherwise only the consensus secondary structure is reported. The consensus secondary structure for a structure bundle is obtained by considering all hydrogen bonds that occur in a minimal number of structures, as defined by the structures parameter. The default is to use all hydrogen bonds that are found in any structure.

The following modes are supported for the output of the results:

classic

Output exactly as in the DSSP publication (Kabsch & Sander, 1983)

normal

Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters.

psipred

Single-line output in the format of the program PsiPred. Helices are indicated by 'H', β-strands by 'E', and all other residues are designated 'C'.

simple

Output only information on helices and β-strands. In the summary line, these are designated '3' for 3₁₀-helices, 'H' for α-helices, and 'B' for β-strands.

ovw

List the secondary structure elements, one per line.

seo

Similar output of the secondary structure elements one per line, separate for helices and β-sheets.