On Tue, Oct 23, 2012 at 3:58 PM, jp d
we are using secondary structure restraints to enforce RNA base pairing. it seems if we use insertion codes , it causes a crash with this error:
/usr/local/phenix-1.8.1-1168/cctbx_project/mmtbx/secondary_structure/bas e_pairing.py", line 508, in identify_base_pairs basecode_1 = atoms[base_1[0]].fetch_labels().resname.strip()[0] IndexError: Index out of range
we are using syntax like this:
refinement.secondary_structure.nucleic_acids { ... base_pair { base1 = segid "WTF" and resseq 80A base2 = segid "WTF" and resseq 96 } }
we also tried putting it in quotes with no luck it works if we use resseq 80
That's because "resseq" selects only for the residue number, without the insertion code. If you want to use 80A, you need to say either "resid 80A" (resid = resseq + icode) or "resseq 80 and icode A". -Nat