The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries.

References:

• Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577-637.

• DSSP Homepage

• Module Name: DSSP (see the modules page for more information)
• Singlethreaded
• Reference structures in /pdb
• Copy of DSSP databank in /fdb/DSSP

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load DSSP
[user@cn3144 ~]$ dssp my-pdb.ent my-ss.dssp

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. DSSP.sh). For example:

#!/bin/bash
module load DSSP
dssp my.pdb my.dssp

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] DSSP.sh

Create a swarmfile (e.g. DSSP.swarm). For example:

dssp ent1.pdb ent1.dssp
dssp ent2.pdb ent2.dssp
dssp ent3.pdb ent3.dssp
dssp ent4.pdb ent4.dssp

Submit this job using the swarm command.

swarm -f DSSP.swarm [-g #] [-t #] --module DSSP