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