Hi, I was thinking along another line, one in which the VC/VD buttons no longer have a purpose. The idea would be to have a text field at the top specifying the time in seconds for one delay block. And then the user only specifies the number of cycles used. For the R1 and R2, this is sufficient. The time for one delay block should never be variable for standard relaxation. The actual relaxation time is calculated by the GUI.
Regards, Edward On 8 June 2011 12:56, Sébastien Morin <[email protected]> wrote: > Hi, > > As Edward mentioned earlier, I think a more general naming for VC/VD might > be better since, anyway, the files are so simple. We should definitely allow > one to use an external file for the list of delays instead of entering them > manually, but I would rather name it differently such that it is more > general. > > Cheers, > > > Séb :) > > > > On 11-06-08 11:45 AM, Michael Bieri wrote: >> >> both files are very simple. >> >> Example of VD: >> >> 0.1 >> 0.4 >> 0.01 >> 0.4 >> ... >> >> >> This is in seconds. >> >> VD: >> >> 1 >> 5 >> 2 >> 8 >> 1 >> ... >> >> >> This is the number the block (CPMG pulse) will be applied. >> >> Both files are plain text files. I can send one tomorrow. >> >> Cheers >> Michael >> >> >> >> Am 08.06.2011 17:20, schrieb Edward d'Auvergne: >>> >>> Ah, for the T2 here, the experiment is the standard one and not the >>> relaxation dispersion version. The delay period is fixed, but the >>> number of CPMG blocks is variable. So it would be VD rather than VC. >>> Do you have an example VD file? >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 8 June 2011 08:55, Michael Bieri<[email protected]> wrote: >>>> >>>> yes, VC is variable counter and VD variable delay. So in T2 experiments, >>>> the >>>> variable delay time can be set directly (in seconds). But for T2 >>>> experiments, the number of the fixed CPMG train is set. The time for >>>> CPMG >>>> pulse is fixed (sum of 180 deg pulse and surrounding delays on hetero >>>> nuc). >>>> I did not add labels to the buttons or the text box, but a help text is >>>> displayed when hovering over with the mouse. >>>> >>>> cheers >>>> >>>> >>>> Am 08.06.2011 16:38, schrieb Edward d'Auvergne: >>>>> >>>>> Good evening :) >>>>> >>>>> Do you know what VC stands for? Variable cycles? And VD is variable >>>>> delays? For R1 and R2, the delay should be fixed and the only >>>>> variable is the number of cycles. What do you think of the user >>>>> giving the length of one cycle in seconds and then specifying the >>>>> number of cycles, with the GUI automatically calculating the >>>>> relaxation delay period? And what is the text field under the +VC >>>>> button? >>>>> >>>>> For the deletion, I was thinking about that. The delete key is >>>>> currently doing nothing, it is not mapped yet. I will try to catch >>>>> that and clear the contents that are highlighted. >>>>> >>>>> Cheers, >>>>> >>>>> Edward >>>>> >>>>> >>>>> On 8 June 2011 08:21, Michael Bieri<[email protected]> wrote: >>>>>> >>>>>> Good morning Edward >>>>>> >>>>>> I assume people are recording T1 and T2 experiments as pseudo 3D >>>>>> spectra >>>>>> (interleaved). The 3rd dimension is a stack of a series of different >>>>>> Tx >>>>>> experiments with varying relaxation delay. The way the relaxation >>>>>> delay >>>>>> is >>>>>> set is to create the VD (T1) or VC (T2) lists. VC lists are just used >>>>>> to >>>>>> set >>>>>> the number of cycles the defined CPMG pulse train will be applied. I >>>>>> think >>>>>> to have the option to read in these lists is very helpful. If people >>>>>> don't >>>>>> know what those lists mean, no problem, just write the values in >>>>>> manually. >>>>>> >>>>>> For the double click. I would like to be able to delete a peak file >>>>>> just >>>>>> by >>>>>> clicking to the grid and deleting the entry (or correcting if file was >>>>>> shifted). This seems not to be possible now. >>>>>> >>>>>> Cheers >>>>>> Michael >>>>>> >>>>>> Am 08.06.2011 15:52, schrieb Edward d'Auvergne: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I'm not sure what VC and VD are exactly. This is cryptic NMR >>>>>>> language, the Varian equivalents will be equally cryptic. Could you >>>>>>> explain these? I would avoid using Bruker notation, or Varian for >>>>>>> that matter, inside of relax. We need to be neutral. >>>>>>> >>>>>>> For the double click idea, I was playing with that yesterday and it >>>>>>> seems to work well with Veto() calls, so I committed it. If we add a >>>>>>> field above to allow the delay time to be set, and a column for the >>>>>>> number of cycles, I think the + and +VD and +VC buttons could all be >>>>>>> eliminated, as they become redundant. I also shifted your code into >>>>>>> gui/components/spectrum.py into the Peak_intensities class, to keep a >>>>>>> cleaner code separation. >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Edward >>>>>>> >>>>>>> >>>>>>> On 7 June 2011 12:47, Michael Bieri<[email protected]> wrote: >>>>>>>> >>>>>>>> Hi >>>>>>>> >>>>>>>> The VD and VC list are not an invention of me. Those list are used >>>>>>>> in >>>>>>>> Bruker >>>>>>>> spectrometers to set the variable delays in T1 and T2 experiments. >>>>>>>> We >>>>>>>> could >>>>>>>> add a wizard, but I think Bruker people know what to do. I have no >>>>>>>> idea >>>>>>>> how >>>>>>>> you set the experiment up on Varians. If somebody knows, we could >>>>>>>> implement >>>>>>>> this as well (to minimise any human introduced errors). >>>>>>>> >>>>>>>> The wx.grid function isn't that advanced. I am not sure if more >>>>>>>> options >>>>>>>> are >>>>>>>> possible (eg button in grid). The double click idea is nice. I will >>>>>>>> implement this. >>>>>>>> >>>>>>>> Cheers >>>>>>>> Michael >>>>>>>> >>>>>>>> Am 07.06.2011 19:32, schrieb Edward d'Auvergne: >>>>>>>>> >>>>>>>>> Hi Michael, >>>>>>>>> >>>>>>>>> I now see what the design is you are trying to achieve :) I.e. you >>>>>>>>> input the time of one relaxation time block and the number of >>>>>>>>> cycles, >>>>>>>>> and relax calculates the times from that. I think that is a good >>>>>>>>> idea! I would suggest to redesign the elements a bit though. >>>>>>>>> >>>>>>>>> - All the buttons and entry boxes on the left of the table could be >>>>>>>>> deleted. >>>>>>>>> >>>>>>>>> - The "relaxation time block [s]" input element could be shifted to >>>>>>>>> the block above, just under the "Unresolved residues:". >>>>>>>>> >>>>>>>>> - A third column added to the grid. >>>>>>>>> >>>>>>>>> - The column names would be "R2 peak lists", "Number of cycles", >>>>>>>>> "Relaxation time [s]". >>>>>>>>> >>>>>>>>> - Double clicking on the first column would open the file open >>>>>>>>> dialog. >>>>>>>>> >>>>>>>>> - Double clicking on the second would allow an integer to be input >>>>>>>>> (and should be checked to be an integer). >>>>>>>>> >>>>>>>>> - The third column would be non-editable and would be automatically >>>>>>>>> calculated when the number of cycles is input (assuming the time is >>>>>>>>> given). >>>>>>>>> >>>>>>>>> What do you think? >>>>>>>>> >>>>>>>>> Cheers, >>>>>>>>> >>>>>>>>> Edward >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 7 June 2011 03:12,<[email protected]> wrote: >>>>>>>>>> >>>>>>>>>> Author: michaelbieri >>>>>>>>>> Date: Tue Jun 7 03:12:32 2011 >>>>>>>>>> New Revision: 12867 >>>>>>>>>> >>>>>>>>>> URL: http://svn.gna.org/viewcvs/relax?rev=12867&view=rev >>>>>>>>>> Log: >>>>>>>>>> Added import VC (variable counter) list function incl. space to >>>>>>>>>> sepcify >>>>>>>>>> counter time. >>>>>>>>>> >>>>>>>>>> Modified: >>>>>>>>>> 1.3/gui/analyses/auto_rx_base.py >>>>>>>>>> >>>>>>>>>> Modified: 1.3/gui/analyses/auto_rx_base.py >>>>>>>>>> URL: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> http://svn.gna.org/viewcvs/relax/1.3/gui/analyses/auto_rx_base.py?rev=12867&r1=12866&r2=12867&view=diff >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ============================================================================== >>>>>>>>>> --- 1.3/gui/analyses/auto_rx_base.py (original) >>>>>>>>>> +++ 1.3/gui/analyses/auto_rx_base.py Tue Jun 7 03:12:32 2011 >>>>>>>>>> @@ -179,6 +179,21 @@ >>>>>>>>>> self.gui.Bind(wx.EVT_BUTTON, self.load_vd, add_vd) >>>>>>>>>> button_sizer.Add(add_vd, 0, wx.ADJUST_MINSIZE, 0) >>>>>>>>>> >>>>>>>>>> + # Add Vc list import >>>>>>>>>> + if self.label =='R2': >>>>>>>>>> + add_vc = wx.Button(self.parent, -1, "+VC") >>>>>>>>>> + add_vc.SetToolTipString("Add VC (variable counter) >>>>>>>>>> list >>>>>>>>>> to >>>>>>>>>> automatically fill in R2 relaxation times.") >>>>>>>>>> + add_vc.SetMinSize((50, 50)) >>>>>>>>>> + self.gui.Bind(wx.EVT_BUTTON, self.load_vd, add_vc) >>>>>>>>>> + button_sizer.Add(add_vc, 0, wx.ADJUST_MINSIZE, 0) >>>>>>>>>> + >>>>>>>>>> + # Time of counter >>>>>>>>>> + label = wx.TextCtrl(self.parent, -1, "0") >>>>>>>>>> + label.SetToolTipString("Time of counter loop in >>>>>>>>>> seconds.") >>>>>>>>>> + label.SetMinSize((50, 20)) >>>>>>>>>> + label.SetFont(wx.Font(7, wx.DEFAULT, wx.NORMAL, >>>>>>>>>> wx.NORMAL, >>>>>>>>>> 0, "")) >>>>>>>>>> + button_sizer.Add(label, 0, 0 ,0) >>>>>>>>>> + >>>>>>>>>> # Pack buttons >>>>>>>>>> sizer.Add(button_sizer, 0, 0, 0) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> relax (http://nmr-relax.com) >>>>>>>>>> >>>>>>>>>> This is the relax-commits mailing list >>>>>>>>>> [email protected] >>>>>>>>>> >>>>>>>>>> To unsubscribe from this list, get a password >>>>>>>>>> reminder, or change your subscription options, >>>>>>>>>> visit the list information page at >>>>>>>>>> https://mail.gna.org/listinfo/relax-commits >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> relax (http://nmr-relax.com) >>>>>>>>> >>>>>>>>> This is the relax-devel mailing list >>>>>>>>> [email protected] >>>>>>>>> >>>>>>>>> To unsubscribe from this list, get a password >>>>>>>>> reminder, or change your subscription options, >>>>>>>>> visit the list information page at >>>>>>>>> https://mail.gna.org/listinfo/relax-devel >>>>>>>>> >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> relax (http://nmr-relax.com) >>>>>>>> >>>>>>>> This is the relax-devel mailing list >>>>>>>> [email protected] >>>>>>>> >>>>>>>> To unsubscribe from this list, get a password >>>>>>>> reminder, or change your subscription options, >>>>>>>> visit the list information page at >>>>>>>> https://mail.gna.org/listinfo/relax-devel >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> relax (http://nmr-relax.com) >>>>>>> >>>>>>> This is the relax-devel mailing list >>>>>>> [email protected] >>>>>>> >>>>>>> To unsubscribe from this list, get a password >>>>>>> reminder, or change your subscription options, >>>>>>> visit the list information page at >>>>>>> https://mail.gna.org/listinfo/relax-devel >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> relax (http://nmr-relax.com) >>>>>> >>>>>> This is the relax-devel mailing list >>>>>> [email protected] >>>>>> >>>>>> To unsubscribe from this list, get a password >>>>>> reminder, or change your subscription options, >>>>>> visit the list information page at >>>>>> https://mail.gna.org/listinfo/relax-devel >>>>>> >>>>> _______________________________________________ >>>>> relax (http://nmr-relax.com) >>>>> >>>>> This is the relax-devel mailing list >>>>> [email protected] >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-devel >>>>> >>>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-devel mailing list >>>> [email protected] >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-devel >>>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-devel mailing list >>> [email protected] >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-devel >>> >>> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel > > -- > Sébastien Morin, Ph.D. > Postdoctoral Fellow, S. Grzesiek NMR Laboratory > Department of Structural Biology > Biozentrum, Universität Basel > Klingelbergstrasse 70 > 4056 Basel > Switzerland > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
