mkhssp does not output

[joaomcteixeira]

Hello,

I have used mkdssp in the past without issues. But today I have downloaded v3.1.5 and installed from scratch. I see that the mkdssp executable does not exist anymore. Or at least it was not created during the installation in my computer.

When I run:

./mkhssp -i SOME.pdb -o some.out

I always get the help message without any other error message, and simply no output is generated.

For example:

(base) joao@vant:~/projects/
$ /home/joao/software/hssp-3.1.5/mkhssp -i 12AS_A.pdb -o out.dssp
mkhssp options:
  -h [ --help ]           Display help message
  -i [ --input ] arg      PDB ID or input PDB file (.pdb), mmCIF file 
                          (.cif/.mcif), or fasta file (.fa/.fasta), optionally 
                          compressed by gzip (.gz) or bzip2 (.bz2)
  -o [ --output ] arg     Output file, optionally compressed by gzip (.gz) or 
                          bzip2 (.bz2). Use 'stdout' to output to screen
  -d [ --databank ] arg   Databank to use (can be specified multiple times)
  -a [ --threads ] arg    Number of threads (default is maximum)
  --min-length arg        Minimal chain length (default = 25)
  --fragment-cutoff arg   Minimal alignment length as fraction of chain length 
                          (default = 0.75)
  -O [ --gap-open ] arg   Gap opening penalty (default is 30.0)
  -E [ --gap-extend ] arg Gap extension penalty (default is 2.0)
  --threshold arg         Homology threshold adjustment (default = 0.05)
  -m [ --max-hits ] arg   Maximum number of hits to include (default = 5000)
  --fetch-dbrefs          Fetch DBREF records for each UniProt ID
  -v [ --verbose ]        Verbose mode
  --version               Show version number and citation info

If I ask for version:

$ /home/joao/software/hssp-3.1.5/mkhssp --version
mkhssp version 3.1.0

If you use HSSP, please cite: 
Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP & Vriend G.
A series of PDB-related databanks for everyday needs.
Nucleic Acids Res. (2015) 43, D364-D368. doi: 10.1093/nar/gku1028.

The original HSSP reference is: 
Sander C & Schneider R.
Database of homology-derived protein structures and the structural meaning of sequence alignment.
Proteins (1991) 9, 56-68. doi: 10.1002/prot.340090107.

I wanted to use the DSSP functionality to extract secondary structure identity from PDBs. Am I missing something obvious?

Thanks for your help

[cbaakman]

@joaomcteixeira for dssp, you need to use the releases in https://github.com/cmbi/dssp. The xssp repository has been split recently.
The version numbers are wrong. We'll update those.

[joaomcteixeira]

Thanks and sorry!
I was actually looking to find the dssp repository but I couldn't, I was looking for xssp. And I had the link saved in my bookmarks and that was what remained has hssp.

Thanks for clarifying!