Hi All,
A couple of enquiries regarding pseudo3D relaxation data. Firstly, how
does one assign using an nmrstar file as I have used to format converter
to import the chemical shifts, ran link resonances and nothing happened,
no assignments appeared on the spectrum and no error messages in the
console:
Python nmrStar reader courtesy of Jurgen Doreleijers (BMRB) - with
modifications added.
Parsing STAR file: /afs/gorlaeus.net/users/s/skinnersp/Pdx/Pdx_assign.str
Done [84] subs with comment at beginning of line
Done [244] subs with comment not at beginning of line
Parsed: [13] datanodes (top level count only)
Created during import: 1 Shift list(s) (with 1126 Shift values)
##########################################################
# Assignments for residue 101, chain 'A' (Val, code 101) #
##########################################################
Set ['Pdx-protein.101.CA'] as single atom
Resonance 'CA' (['Pdx-protein.101.CA']) -- RS -- 'CA' -- 'CA' atom(s)
Set ['Pdx-protein.101.CB'] as single atom
Resonance 'CB' (['Pdx-protein.101.CB']) -- RS -- 'CB' -- 'CB' atom(s)
Set ['Pdx-protein.101.CG1'] as normal prochiral (stereo)
Resonance 'CG1' (['Pdx-protein.101.CG1']) -- RS -- 'CG1' -- 'CG1'
atom(s)
Set ['Pdx-protein.101.CG2'] as normal prochiral (stereo)
Resonance 'CG2' (['Pdx-protein.101.CG2']) -- RS -- 'CG2' -- 'CG2'
atom(s)
Set ['Pdx-protein.101.H'] as single atom
Resonance 'H' (['Pdx-protein.101.H']) -- RS -- 'H' -- 'H' atom(s)
Set ['Pdx-protein.101.HA'] as single atom
Resonance 'HA' (['Pdx-protein.101.HA']) -- RS -- 'HA' -- 'HA' atom(s)
Set ['Pdx-protein.101.HB'] as single atom
Resonance 'HB' (['Pdx-protein.101.HB']) -- RS -- 'HB' -- 'HB' atom(s)
Set ['Pdx-protein.101.HG1'] as deep prochiral (stereo)
Resonance 'HG1*' (['Pdx-protein.101.HG1']) -- RS -- 'HG1*' --
'HG11,HG12,HG13' atom(s)
Set ['Pdx-protein.101.HG2'] as deep prochiral (stereo)
Resonance 'HG2*' (['Pdx-protein.101.HG2']) -- RS -- 'HG2*' --
'HG21,HG22,HG23' atom(s)
Set ['Pdx-protein.101.N'] as single atom
Resonance 'N' (['Pdx-protein.101.N']) -- RS -- 'N' -- 'N' atom(s)
Secondly, how does one import a pseudo3D relaxation experiment with the
delays in the Z dimension. That data is in nmrPipe format and in ucsf
format. In the past with bruker data, a dialogue box appeared asking if
the experiment was pseudo3D or not, with these experiments it doesn't.
Any ideas on this.
Thanks in advance
Simon
--
Simon P Skinner
Protein Chemistry Group
Leiden Institute of Chemistry, Universiteit Leiden
Phone: +31 71 527 6089 / Fax: +31 71 527 4349
E-mail : [log in to unmask]
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