[phenixbb] RNA base pairs with insertions

jp d yoyoq at yahoo.com
Tue Oct 23 15:58:53 PDT 2012

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:

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


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