Query about hhalign

[hrp1000]

:exclamation: Make to check out our User Guide.

Expected Behavior

break in sequence where it occurs in PDB file (i.e. between Arg221 & Gln 251 in my test file)

Current Behavior

break in sequence one residue before where I'd expect - between Arg 220 & residue 250 (which doesn't exist in my input PDB - in attached zip file).

I notice that the version of hhalign I'm using seems to be dated 2007 - very possible that this is the root of the problem.

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps. ~/HH/hhalign -i ~/harry/query.hhm -t /~/harry/userpdb.hhm -loc -ssm 2 -ssw 0.1 -aliw 60 -o ~/harry/alignment.txt

HH-suite Output (for bugs)

Please make sure to post the complete output of the tool you called. Please use gist.github.com. see alignment.txt

Context

Providing context helps us come up with a solution and improve our documentation for the future. Running as part of Phyre2 - so hhm files produced by hh-suite

Your Environment

Include as many relevant details about the environment you experienced the issue in.

• Version/Git commit used:-bash-4.2$ ./hhalign -h

HHalign version 1.5.0 (November 2007)

• Server specifications (especially CPU support for AVX2/SSE and amount of system memory): see attached file "cpuinfo.txt"
• Operating system and version: more /etc/redhat-release CentOS Linux release 7.5.1804 (Core)

hhalign.zip alignment.txt cpuinfo.txt

[hrp1000]

Just checked with version 3.3.0 (built last August) - I get the same issue, i.e. the gap is shifted by one amino acid.

[hrp1000]

Also tried with .hhm file created from a .fasta file with the "missing" residues represented with "-". Same result - the gap in the alignment is shifted by one residue.

[hrp1000]

Any response of any kind would be gratefully received!