I would really like to see the peak handling improved in analysis - I have
long been asking for peaks to have a "footprint" defined by e.g. linewidth
in each dimension. Not only would this be useful for quantitation, but
also for more complete use of e.g. overlapped NOESY data for chemical
shift matching etc.
Converting from Numeric to NumPy is typically not too difficult.
Brian
On Fri, 30 Nov 2012, Wayne Boucher wrote:
> Hello,
>
> That looks like one possibility (but it is using a now obsolete package
> called Numeric).
>
> Wayne
>
> On Thu, 29 Nov 2012, Paul Schanda wrote:
>
>> Hello,
>>
>> I will finally end up using nmrPipe for quantitative analysis rather than
>> CCPN, as I find the constant box size not
>> ideal. It is a pity, though, as changing programs on the way is always
>> complicated.
>>
>> It would be really great if the quantitative accuracy with which
>> intensity/volume data can be retrieved from within
>> CCPN was improved.
>> It might be a good idea to include existing programs into CCPN to do this
>> job.
>> For example, there is a good (and entirely python-based) program for this:
>>
>> http://pound.med.utoronto.ca/~flemming/fuda/
>>
>> How complicated would it be to incorporate this into CCPN?
>>
>> Paul
>>
>>
>>
>> Am 27.11.2012 um 17:26 schrieb Wayne Boucher <[log in to unmask]>:
>>
>> Ah, good that that button does what you want.
>>
>> But anything you can do with that data in a separate script can be
>> done with the same script inside
>> Analysis, modified to get hold of the data that is being exported
>> directly in memory rather than via a
>> file. But if you are happy to export first that will likely be the
>> easiest option for you.
>>
>> Wayne
>>
>> On Tue, 27 Nov 2012, Paul Schanda wrote:
>>
>> Hello,
>>
>> This variable box width is being implemented in v3 of
>> Analysis (we
>> know it's been a sore point).
>> Very much looking forward to v3 for several aspects.
>>
>> If you are willing to use Python/Numpy instead of Matlab
>> then you
>> could write the whole thing directly as a macro which
>> could be run
>> from inside Analysis.
>> How would one do that? I can do it in Numpy, no problem.
>> However, the analysis is
>> somewhat involved, it includes doing a grid search of the
>> experimental
>> intensity/volume change against a grid of simulated evolution
>> curves (simulated
>> with yet something else than python, but can be loaded into
>> python).
>> It seems like the easiest for me might be to get the data out
>> of CCPN, and then do
>> my things in ipython/numpy. But for curiosity: how would one
>> include such python
>> scripts.
>>
>> Back on the residue issue, I assume you mean you want it
>> by residue
>> for a specific peak list. But even then, the same atom
>> can appear
>> multiple times. Do you want every single volume for any
>> peak for a
>> given residue, and if so how do you want this annotated,
>> by peak
>> serial??? So should each line in effect be:
>>
>> residue, (volume1, peakserial1), (volume2, peakserial2),
>> etc.
>> I just figured out that the "Export Data" button in "Data
>> Analysis : Follow
>> Intensity Changes" does pretty much what I want. So that's
>> solved.
>> regards
>> paul
>>
>> Wayne
>>
>> On Tue, 27 Nov 2012, Paul Schanda wrote:
>>
>> Dear Wayne,
>>
>> thanks for the information.
>>
>> The fixed box width for the whole spectrum is
>> probably a
>> considerable drawback for quantitative measurements.
>> Essentially, this
>>
>> It would be nice to have variable box widths in
>> future
>> versions ("just" another attribute to each peak, in
>> addition to the frequencies). It would also be nice
>> if the
>> box sizes were displayed on the spectrum, instead of
>> having only the crosses.
>>
>> (3) That sounds like a job for a macro. So
>> currently you can export the Peak List data
>> which includes the volume, but that is one
>> volume per line of course and you want all the
>> atoms to be together on one line. Actually,
>> when you say "fit externally" do you want the
>> actual data points in the neighbourhood of the
>> maximum?? (Another macro job to extract
>> those.)
>>
>> No, i want to take the peak volumes as a function of
>> mixing time and fit some function to those (using
>> Matlab
>> or Python scripts). So I would just need the script
>> that
>> gives me for each residue and each mixing time the
>> corresponding peak volume.
>>
>> Paul
>>
>> Wayne
>> ***************************
>> Paul Schanda
>> [log in to unmask]
>>
>>
>>
>>
>> ***************************
>>
>> Paul Schanda
>> [log in to unmask]
>>
>>
>>
>>
>>
>
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
----------------------------------------------------------------------
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