The final HELIXCAP HMM models, along with the code to generate and cross-verify the HELIXCAP code and the relevant source files, is attached. The HMMs were generated using HMMer 2.3, but should be compatible with HMMer 3. HELIXCAP-align-9-1.hmm and HELIXCAP-align-9-2.hmm were generated with the 25% and 75% clustering cutoffs, respectively. 

To use the HELIXCAP model, use the standard HMMer command
hmmsearch --forward \"$hmmFileName\" \"$sequences\" > \"$output\"
where $hmmFileName, $sequences, and $output are the HMM, sequences to scan, and output file, respectively.

To generate a HELIXCAP model requires modifying the code to specify the locations of the PDBminus (the minus file used from 10/12/07 is attached) and the HMMer binaries. (This DOES require HMMer 2.3 to work, as the settings have changed in HMMer 3.) GetOpt::Long and IO::Handle are dependencies. The perl invocation will require the names of each of the files used to generate positive and negative controls, as well as the database of available clusters. For model 9-1, for instance, these are:

-c Ncap-v3-e60-StartStructBlastNoDupe-25.clust 
(pre-processed cluster database)
-s: Ncap-v3-e60-StartStructBlastNoDupe.fasta 
(corresponding sequence set)
-i Ncap-v3-leftright.hmm 
(initial HMM from DALI data)
-h helixcap-align-9-1.hmm 
(HMM containing full model)
-o helixcap-align-9-1.out 
(human-readable output file with statistics)
-l helixcap-align-9-1.txt 
(log file with machine-readable statistics output)
-t Ncap-leftright-nums.txt 
(test file with additional sequences not in 2007 set to additionally test reliability)

an optional switch -E allows the cutoff value to be frobbed.