Subject: problem using sparky2bmrb.py
From: Siavoush
Date: Mar 17, 2010

Previous: 656

Dear list,

I am trying to use sparky2bmrb.py and bmrb.py scripts, but I am geting the following error messages. Here are what I have entered in the command line for stand alone version of the script, and the messages I got back. I will appreciate any help.

Cheers, Siavoush

proton.mmb.usyd.edu.au.siavoush:132 ~/bin/sparky2bmrb.py --C=0.2 --N=0.2 --H=0.02 -o myfile.bmrb template.star myshift.shifts

Template NRM STAR file reading ..............................
Please enter your sequence in one-letter code :
YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVCEQDIYEWTKINGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAANGIDDE

Sparky chemical shift list reading ..........................

Atom name conversion to IUPAC nomenclature...................

translation from XPLOR to IUPAC nomenclature

ambiguity code assignment
- default ambiguity code 2 : -CH2, -CH3, -NH2 and -NH3
- default ambiguity code 3 : aromatic C and H from Y and F
- default ambiguity code 4 : HH1[12], HH2[12] from R

atom retrieval
Traceback (most recent call last):
File /home/siavoush/bin/sparky2bmrb.py, line 585, in ?
assign_ambiguity(sparky[rank])
File /home/siavoush/bin/sparky2bmrb.py, line 514, in assign_ambiguity
residue = res_dict.values()[0].res
IndexError: list index out of range