[phenixbb] RNA base pairs with insertions

[Nathaniel Echols]

On Tue, Oct 23, 2012 at 3:58 PM, jp d <yoyoq at yahoo.com> wrote:
> 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