[modeller_usage] How to get Secondary Structure in Alignment file

Dear Modellers, Suppose i have two templates, and a target sequence. Instead of sequence alignment based file, i want to consider the secondary structure information, like given below

Template1> HCSIHISC Template2> HCSHHISC

H=Helix, C=Coil, S-Strand, I=Indels

Is it possible to get the alignment in this case for multiple templates against the target sequence( whose structure can also be represented as best aligned folds)

Thanks Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA