[phenixbb] RNA base pairs with insertions
jp d
yoyoq at yahoo.com
Tue Oct 23 15:58:53 PDT 2012
hi,
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 78
base2 = segid "WTF" and resseq 98
}
base_pair {
base1 = segid "WTF" and resseq 79
base2 = segid "WTF" and resseq 97
}
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
this is with version
Version: 1.8.1
Release tag: 1168
thanks
jpd
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