Dear MMBians, I am trying to thread around a section (nucleotides 57-91) of wheat 18S ribosomal RNA (3IZ7) using MMB_2.13. For some reason, instead of a hairpin I always get a straight helix. Strangely the target PDB file which is set rigid also becomes a linear molecule in the resulting PDB output. Can someone help me trouble shoot? I am attaching the command file, target pdb model and output pdb for you to see. Target pdb chain A: 3IZ7-57-91.pdb Command file threaded chain X: commands.3IZ7-threading-57-91.dat Result PDB: Sbi-16S-57-91 I appreciate your time and input, Uzay Sezen Uğur Uzay Sezen Post-Doctoral researcher Plant Genome Mapping Laboratory University of Georgia Center for Applied Genetic Technologies 111 Riverbend Rd., Athens, GA 30602 uzay@uga.edu<mailto:uzay@uga.edu> tel: 706-583-0170<tel:706-583-0170> fax: 706-583-8120<tel:706-583-8120> http://www.plantgenome.uga.edu/ http://naturedocumentaries.org/