I am quite new to MODELLER and I would like to know if it is possible to to models a protein having with few trans-membrane (TM) regions. Are there such an example or tutorial available? I tried to search archive but, unfortunately, there was nothing that can help me. Is it possible to assign a few TM regions (in the form of restrain or something like that) which would be modeled in a plane. Any suggestions/inputs related to modelling enzyme having TM regions will be appreciated. My system has very poor similarity (< 20 %) in PDB, and also no similarity between TM regions of query and TM regions of proteins in PDB.