Subject: Re: Sequence function
From: ethernet3399
Date: Nov 8 6:23 PM
Previous: 27
Sorry for my less experience, I didnt use the atomnames.py
extension before.
But as I know, sparky dont check the protein/DNA/RNA name. While
you do the assignment, you mark the peak what you like. Then you can
change it by re-assign, or use the command rr to re-name one atom,
or re-name one residue/nucleotide.
So you can start the assignment, and later change your RNAs name
according to some standard nomenclature.
May this help.
Tieying Zhang
at SIBS
--- In nmr_sparky@yahoogroups.com , m_randir m_randir@y... wrote:
Hello all. I have been unable to get sparky to accept an RNA
sequence. Using atomnames.py as a guide I input the one-letter
residues codes. When I click OK a shell window opens with the
following errors:
Exception in Tkinter callback
Traceback (most recent call last):
File c:Program Filessparkypythonlib-tkTkinter.py, line
1345,
in __call__
return self.func(*args)
File c:Program Filessparkypythonsparkysequence.py, line
78,
in ok_cb
seq = self.read_sequence()
File c:Program Filessparkypythonsparkysequence.py, line
71,
in read_sequence
s = sequence(aa_sequence, first_residue_number)
File c:Program Filessparkypythonsparkysequence.py, line
163,
in __init__
self.resonances = self.create_resonances()
File c:Program Filessparkypythonsparkysequence.py, line
192,
in create_resonances
for atom_name in atomnames.protein_atoms_by_group[symbol]:
KeyError: U
Exception in Tkinter callback
Traceback (most recent call last):
File c:Program Filessparkypythonlib-tkTkinter.py, line
1345,
in __call__
return self.func(*args)
File c:Program Filessparkypythonsparkysequence.py, line
78,
in ok_cb
seq = self.read_sequence()
File c:Program Filessparkypythonsparkysequence.py, line
71,
in read_sequence
s = sequence(aa_sequence, first_residue_number)
File c:Program Filessparkypythonsparkysequence.py, line
163,
in __init__
self.resonances = self.create_resonances()
File c:Program Filessparkypythonsparkysequence.py, line
192,
in create_resonances
for atom_name in atomnames.protein_atoms_by_group[symbol]:
KeyError: U
Does sparky assume I have an amino acid sequence? How can this be
fixed? Any input would be much appreciated.
By the way, I was very happy to find this group and hope to
contribute
at least as much as I take.
Thanks in advance,
m_randir