> I wish to output a table containing each peaks chemical shift, assignment
> and molecular system.
>
> Using edit peak list I can export the table, however the details column only
> shows the molecular system after clicking edit peak and then update.
>
> This has to be done for each individual peak.
>
> Is it possible to change this to automatically show the molecular system or
> for the whole table to be updated in one go?
Hi Jed,
Just realised, no one replied to this query.
Anyhow, it is fairly easy to put a MolSystem annotation into the details
field of a peak, but you could do one of two things:
Generally, a whole peaklist's experiment is associated with a molecular
system (or possibly more than one), so all the peaks in the entire list
are linked to this same molSystem in which case the annotation would be
idential for each peak. The fact that there is normally only ever one
molSystem for an entire list is the reason why it is generally not
annotated.
Alternatively, you could annotate only those peaks which are specifically
assigned to an atom in a given molSystem. Assuming this is what you would
want, at the command line you could try:
-------------------------------------------------------------------------------
peakList = top.argumentServer.getPeakList()
for peak in peakList.peaks:
molSystems = set()
for peakDim in peak.peakDims:
for contrib in peakDim.peakDimContribs:
resonanceSet = contrib.resonance.resonanceSet
if resonanceSet:
atom = resonanceSet.findFirstAtomSet().findFirstAtom()
molSystems.add(atom.residue.chain.molSystem)
molSystemCodes = [ms.code for ms in molSystems]
molSystemCodes.sort()
peak.details = ','.join(molSystemCodes)
-------------------------------------------------------------------------------
T.
-------------------------------------------------------------------------------
Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.pantonia.co.uk
-------------------------------------------------------------------------------
------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- -------
-------------------------------------------------------------------------------
|