Rasmus Fogh wrote:
>Dear Gary,
>
>If you have two chains that are not symmetrical, you should assign the two
>chains explicitly. So, a peak that could come from either chain (or, in
>practice, both) should be assigned as ambigous, with two resonances on
>each dimension.
>
Yes I am doing this so I have resonances for chain A H and chain A N and
chain B H and chain B N. However, should these reonances be in separate
PeakContribs?
so using a slightly mangled syntax, consider the case below
peak[1].peakDims[1].peakDimContribs[0] = <PeakDimContrib for reonance A H >
<PeakDimContrib for reonance A H >.resonance = <resonance A H>
peak[1].peakDims[1].peakDimContribs[1] = <PeakDimContrib for reonance B H >
<PeakDimContrib for reonance B H >.resonance = <resonance B H>
peak[1].peakDims[1].peakDimContribs[0] = <PeakDimContrib for reonance A N >
<PeakDimContrib for reonance A N >.resonance = <resonance A N>
peak[1].peakDims[1].peakDimContribs[1] = <PeakDimContrib for reonance B N >
<PeakDimContrib for reonance B N >.resonance = <resonance B N>
now should I have
peak[1].PeakConribs[0] = [<PeakDimContrib for reonance A H >,
<PeakDimContrib for reonance B H >, <PeakDimContrib for reonance A N >,
<PeakDimContrib for reonance B N >]
or should I have
peak[1].PeakConribs[0] = [<PeakDimContrib for reonance A H >,
<PeakDimContrib for reonance A N >](with weight 0.5)
peak[1].PeakConribs[1] = [<PeakDimContrib for reonance B H >,
<PeakDimContrib for reonance B N >](with weight 0.5)
where A and B are chain identifiers and H and N are atoms..
Further to this
1. if I have a peak which I know is residue 13 but I don't know what the
chain assignment for the peak is what should my my setup be then, whould
it be:
peak[1].PeakConribs[0] = [<PeakDimContrib for reonance A H >,
<PeakDimContrib for reonance A N >](with weight 0.0)
peak[1].PeakConribs[1] = [<PeakDimContrib for reonance B H >,
<PeakDimContrib for reonance B N >](with weight 0.0)
2. do all assignments arising from the combinatorial nature of a
peakContrib have to be reasonable? Thus for example you can have an
overlapped hcch-tocsy peak where the 13C and 1H resonances are
overlapped but you know for example what some of the indirect proton
shifts come from one residue and the rest from another. What should you
do then two separate peakcontribs with the subsets in them and weights
of 0...
3. (most probably for the ccpn team) This is clearly complicated and I
am not sure i follow the implications and reasoning in all cases. Can
you expand on why the peakcontrib is there and what it's practical uses
are in the round covering the common cases...
regards
gary
> A bit of a pain, i know.
>
>Yours,
>
>Rasmus
>
>---------------------------------------------------------------------------
>Dr. Rasmus H. Fogh Email: [log in to unmask]
>Dept. of Biochemistry, University of Cambridge,
>80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
>
>On Tue, 2 May 2006, Gary S. Thompson wrote:
>
>
>
>>Dear All
>> I am assigning a dimer which in its unbound state has two fold
>>symmetry. However, once I bind a ligand to it some of the symmetry (but
>>not all) is lost. Thus I end up with peaks in my 1H-15N hsqc some of
>>which are for A subunits and some of which are for B and some of which
>>are for A and B. In the case of the A+B peaks degenerate peaks should
>>each pair orf resonances from the two two dimensions and a sigle chain
>>be in separate peakContribs....
>>
>>Also another question which is related. Programmatically what is the
>>quickest way to identify sets of identical chains in a molecular system?
>>Do I need to do a sequence comparison ever time I search for a repeat of
>>the same chain...
>>
>>regards
>>gary
>>
>>--
>>-------------------------------------------------------------------
>>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
>>-------------------------------------------------------------------
>>
>>
>>
>
>.
>
>
>
--
-------------------------------------------------------------------
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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