INFO on how to scan a FASTA file with Gene3D HMM models resolve Domain Architectures.
(The methods have been tested on hmmer v3.1b2 python2.*)


#First of all extract the HMM models TAR archive
tar -xvf hmms.tar.gz

#run hmmsearch on sequence file, change parameters as appropriate
hmmsearch -Z  10000000  --domE 0.001 --incdomE  0.001  -o seqs.hmmsearch    hmms/main.hmm   seqs.fa

#resolve any conflicting (overlapping) domain assignments, versions for different platforms (mac/linux) are available online along with documentation:
# http://cath-tools.readthedocs.io/en/latest/tools/cath-resolve-hits/
# we recommend using a worst-permissible-bitscore of 25 and applying --min-dc-hmm-coverage=80 (only available for processing hmmsearch output) 


./cath-resolve-hits --min-dc-hmm-coverage=80 --worst-permissible-bitscore 25 --output-hmmer-aln --input-format  hmmsearch_out seqs.hmmsearch > seqs.crh


#assign CATH superfamilies to the output file generated by cath-resolve-hits
(in the future it is likely that this functionality will move into the cath-resolve-hits tool)
python ./assign_cath_superfamilies.py seqs.crh