On 06/08/2010 05:11 PM, Wim Vranken wrote:
> Hi Gary,
>
>
>> Does the ebi export system correct set ambiguity codes in its
>> exported nmr star files? If so how can I get it work as all my
>> ambiguity codes are 1...
>>
> It definitely writes out '2' for non-stereospecifically assigned
> prochirals in the full NMR-STAR 3.1 exporter, but older code to write
> out the 2.1.1 snippet might not... how do you write out the file?
>
> Wim
>
Hi wim
I have updated to the latest release and still have an ambiguity code
of 1 for all exported chemical shifts
e.g.
stop_
loop_
_Atom_chem_shift.ID
_Atom_chem_shift.Assembly_atom_ID
_Atom_chem_shift.Entity_assembly_ID
_Atom_chem_shift.Entity_ID
_Atom_chem_shift.Comp_index_ID
_Atom_chem_shift.Seq_ID
_Atom_chem_shift.Comp_ID
_Atom_chem_shift.Atom_ID
_Atom_chem_shift.Atom_type
_Atom_chem_shift.Atom_isotope_number
_Atom_chem_shift.Val
_Atom_chem_shift.Val_err
_Atom_chem_shift.Assign_fig_of_merit
_Atom_chem_shift.Ambiguity_code
_Atom_chem_shift.Occupancy
_Atom_chem_shift.Resonance_ID
_Atom_chem_shift.PDB_record_ID
_Atom_chem_shift.PDB_model_num
_Atom_chem_shift.PDB_strand_ID
_Atom_chem_shift.PDB_ins_code
_Atom_chem_shift.PDB_residue_no
_Atom_chem_shift.PDB_residue_name
_Atom_chem_shift.PDB_atom_name
_Atom_chem_shift.Auth_entity_assembly_ID
_Atom_chem_shift.Auth_seq_ID
_Atom_chem_shift.Auth_comp_ID
_Atom_chem_shift.Auth_atom_ID
_Atom_chem_shift.Details
_Atom_chem_shift.Entry_ID
_Atom_chem_shift.Assigned_chem_shift_list_ID
*
20 . 1 1 11 11 GLY HA2 H 1 3.975 0.004 . 1 . 20 . . . . . . . . . . . . 1 1
21 . 1 1 11 11 GLY HA3 H 1 3.864 0.002 . 1 . 21 . . . . . . . . . . . . 1 1
...
117 . 1 1 17 17 LEU HD11 H 1 0.862 0.005 . 1 . 111 . . . . . . . . . . . . 1 1
118 . 1 1 17 17 LEU HD12 H 1 0.862 0.005 . 1 . 111 . . . . . . . . . . . . 1 1
119 . 1 1 17 17 LEU HD13 H 1 0.862 0.005 . 1 . 111 . . . . . . . . . . . . 1 1
120 . 1 1 17 17 LEU HD21 H 1 0.859 0.004 . 1 . 112 . . . . . . . . . . . . 1 1
121 . 1 1 17 17 LEU HD22 H 1 0.859 0.004 . 1 . 112 . . . . . . . . . . . . 1 1
122 . 1 1 17 17 LEU HD23 H 1 0.859 0.004 . 1 . 112 . . . . . . . . . . . . 1 1
(I have marked the _Atom_chem_shift.Ambiguity_code with a star it
should be column 14)
do you have any suggestions?
regards
gary
--
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Dr Gary Thompson [Homans Lab Research Coordinator]
Astbury Centre for Structural Molecular Biology,
University of Leeds,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: [log in to unmask] Fax +44-113-3431935
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