Tim Stevens wrote:
>Dear all,
>
>I'm planning a new section within Analysis to deal with quality control
>for assignments, so I'm canvasing opinion for the features that should be
>included. Here is my preliminary list of things to check and display in
>tables for mending etc. Let me know if you think that there is anything
>else I should consider or any specific requirements for my current list.
>
>
> * Resonance shifts with large standard deviations
>
> * Peaks assignments that match shift values poorly
>
> * Assigned peaks with 'unusual' intensities
>
> * Assignments that would match peak positions better if prochiral
> resonances were swapped
>
> * 1H resonances that have more than one 'onebond' partner
>
> * Atomic assignments that are outside usual BMRB chemical shift ranges
>
> * % assignment categorised by backbone side chain etc
>
>
>T.
>
>
>
>
Hi Tim
I have written some code to check triple resonance peak lists (you
may consider this as trivial, there maybe better ways to do these things
or this maynot be within the remit of this problem) specifically for an
HSQC HNCA pair of spectra I have checked
hnca peaks with too few resonances from the parent hsqc spectrum
peaks in an hsqc missing resonances in one or other dimension
peaks in an hsqc with with resonances that don't share the same spin system
peaks with resonances not in the same peak in the parent hsqc peak list
peaks with the wrong cardinality
hnca peaks with only one parent resonance
I planned to add checks for peaks that don't match the parent peak
position and to check for strips with to many peaks in HCCH type
spectra for the assigned residue
As a suggestion many of these problems have fairly standard quick fixes
which could be catered for by a few buttons... (however wgat I have at
the moment is very crude and text based.
regards
gary
>-------------------------------------------------------------------------------
> Dr Tim Stevens Email: [log in to unmask]
> Department of Biochemistry [log in to unmask]
> University of Cambridge Phone: +44 1223 766022 (office)
> 80 Tennis Court Road +44 7816 338275 (mobile)
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> Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
> United Kingdom http://www.pantonia.co.uk
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>
--
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Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: [log in to unmask] Fax +44-113-2331407
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