Ah, right, that's the non-single-scan interleaved proteinpack
experiment I used almost a decade ago. Now I remember doing
single-fid interleaving on that, setting relaxT to an array. From
memory the time period within the R2 (or maybe R1) is slightly
different from what the pulse sequence says. That may be fixed now,
but is easy to calculate by summing all the pulse times and delays in
the single block.
This has a number of cycles associated with it, but the user
integrates it into relaxT. ncyc is then back calculated from relaxT,
e.g.:
if (T2[A]=='y')
{
dec2phase(zero);
initval(0.0,v3); initval(180.0,v4);
ncyc = 100.0*relaxT;
initval(ncyc,v5);
So in this case in the GUI, maybe we should have both the raw
relaxation time and ncyc settable. I could swap the two columns last
columns, and make the relaxation time field editable. If the time for
the block is set, I would make that column read only so that only ncyc
can be set. Could this design be improved?
Cheers,
Edward
On 14 June 2011 11:18, Sébastien Morin <[email protected]> wrote:
> Hi Ed,
>
> Attached (in a tar archive) are a Varian Biopack HSQC pulse sequence and the
> corresponding procpar for recording of T2.
>
> The parameters to look for in the procpar are the following:
> T2 -> set to "y" in order to record T2
> relaxT -> set to 0.11 for a 110 ms relaxation delay
>
> Please note that relaxT is limited to some values, as it depends on the
> building blocks used to make the relaxation delay...
>
> In the case of R1 (T1), the principle is exactly the same with T1 set to "y"
> and relaxT set to the desired value (although also with some limitations).
>
> Cheers,
>
>
> Séb :)
>
>
> On 11-06-14 11:00 AM, Edward d'Auvergne wrote:
>>
>> Hi,
>>
>> I'm really just playing at the moment with these things. I'm also
>> looking at making the interface expandable so that the main GUI window
>> can be resized. This would be of great use in the next version of the
>> interface, and it also adds a lot of polish. I'm also abstracting the
>> code a lot so that all similar GUI elements are located within one
>> method (or class). Then that one piece of code can be improved or
>> modified and that change is propagated across the GUI. For example
>> the 'change' button, or the text-textctrl-button GUI elements.
>>
>> For the pulse sequences, would you be able to attach the one where the
>> times are set directly? I have used the Varian protein-pack (now
>> called Biopack I think) and Kay's single scan interleaved sequences,
>> and have extensively worked with Paul Gooley and Wolfgang Bermel to
>> have single scan interleaving and temperature compensation blocks
>> added to the standard Bruker sequences. From all this work, there are
>> only two things I see that are set in these sequences:
>>
>> 1) The length of time of one CPMG block (in the R2) or the length of
>> the relaxation period with cross-correlated relaxation decoupling in
>> the R1.
>>
>> 2) The number of cycles (protein-pack) or the relaxation delay loops
>> (Bruker).
>>
>> I have yet to come across a pulse sequence where you can specify times
>> randomly, e.g. 10ms, 176.23 ms, 18 ms, 206.46 ms (it may be possible
>> though). Protein-pack's, Kay's, and Bruker's sequences all calculate
>> what the time periods are from the single element time, multiplied by
>> the number of times it is repeated (though sometimes slightly off).
>> For example in Bruker Biospin, see the d20 loop in:
>>
>> http://rmni.iqfr.csic.es/guide/eNMR/proteins/relaxexp1.html
>>
>> If you have a pulse sequence where the times are set directly, could
>> you attach it? There is a possibility that the R1 time can be
>> anything, and in that case we can redesign the GUI element to fit.
>> But this is dangerous as the cross-correlated relaxation decoupling
>> may not be consistent if pulses are not perfectly calibrated. It is
>> most definitely not allowed in a R2 experiment.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> On 14 June 2011 01:31, Michael Bieri<[email protected]> wrote:
>>>
>>> Hi Edward
>>>
>>> I think we will have to change this design. Currently, R1 tab is wrong,
>>> as
>>> nobody sets cycles for T1 delays. Here, relaxation delays have to be set
>>> directly.
>>> For R2, this is true for Bruker people. But I don't know if Varian sets
>>> the
>>> T2 delays in a similar matter (using cycles). So we might exclude Varian
>>> users like this...
>>>
>>> Let me know when you finalised the reorganisation of the GUI components
>>> and
>>> I will fix this.
>>>
>>> By the way. Nice coding around the grid class! I like the spin.ctrl in
>>> the
>>> grid!
>>>
>>> Cheers
>>> Michael
>>>
>>> Am 10.06.2011 23:57, schrieb [email protected]:
>>>>
>>>> Author: bugman
>>>> Date: Fri Jun 10 15:57:28 2011
>>>> New Revision: 12975
>>>>
>>>> URL: http://svn.gna.org/viewcvs/relax?rev=12975&view=rev
>>>> Log:
>>>> The peak intensity GUI element is now enclosed within a StaticBox.
>>>>
>>>>
>>>> Modified:
>>>> 1.3/gui/components/spectrum.py
>>>>
>>>> Modified: 1.3/gui/components/spectrum.py
>>>> URL:
>>>>
>>>> http://svn.gna.org/viewcvs/relax/1.3/gui/components/spectrum.py?rev=12975&r1=12974&r2=12975&view=diff
>>>>
>>>>
>>>> ==============================================================================
>>>> --- 1.3/gui/components/spectrum.py (original)
>>>> +++ 1.3/gui/components/spectrum.py Fri Jun 10 15:57:28 2011
>>>> @@ -241,16 +241,22 @@
>>>> # The number of rows.
>>>> self.num_rows = 50
>>>>
>>>> - # Add peak list selection header.
>>>> - self.subparent.add_subtitle(box, "Data points")
>>>> + # A static box to hold all the widgets, and its sizer.
>>>> + stat_box = wx.StaticBox(self.parent, -1, "Peak lists")
>>>> + stat_box.SetFont(self.gui.font_subtitle)
>>>> + sub_sizer = wx.StaticBoxSizer(stat_box, wx.VERTICAL)
>>>>
>>>> # Add the cycle delay time element.
>>>> - self.delay_time = self.subparent.add_text_sel_element(box,
>>>> self.parent, text="Single delay cycle time [s]")
>>>> + sub_sizer.AddSpacer(self.spacing)
>>>> + self.delay_time =
>>>> self.subparent.add_text_sel_element(sub_sizer,
>>>> self.parent, text="Single delay cycle time [s]")
>>>>
>>>> # Add the grid.
>>>> - box.AddSpacer(self.spacing)
>>>> - self.add_grid(box)
>>>> - box.AddSpacer(self.spacing)
>>>> + sub_sizer.AddSpacer(self.spacing)
>>>> + self.add_grid(sub_sizer)
>>>> + sub_sizer.AddSpacer(self.spacing)
>>>> +
>>>> + # Add the sizer to the static box and the static box to the
>>>> main
>>>> box.
>>>> + box.Add(sub_sizer, 1, wx.ALL|wx.EXPAND, 0)
>>>>
>>>>
>>>> def add_buttons(self, sizer):
>>>>
>>>>
>>>> _______________________________________________
>>>> relax (http://nmr-relax.com)
>>>>
>>>> This is the relax-commits mailing list
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>>>>
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>>>>
>>>>
>>> _______________________________________________
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>>>
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>> _______________________________________________
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>>
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>
> --
> Sébastien Morin, Ph.D.
> Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> Department of Structural Biology
> Biozentrum, Universität Basel
> Klingelbergstrasse 70
> 4056 Basel
> Switzerland
>
>
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