Sorry, I meant the hidden, dimensionless radian unit!
On Thu, Jan 8, 2009 at 10:58 AM, Edward d'Auvergne <[email protected]> wrote: > Seb, > > I might send a seperate message explaining the hidden, unitless radian > unit. All the relaxation dispersion equations and their parameters > are in radial units, and therefore care has to be taken when setting > or using the input and output values. I.e. rotational correlation > times are in s/rad, kex is in rad/s, R2 is in rad/s, etc. This is why > using published NMR data from the literature would be very useful for > the system test - relax in the end should match the published values. > This test, or maybe a few tests, will be very useful for determining > if relax is returning rubbish or good results. If relax can't be made > to match certain published results, it may even uncover incorrect > published data ;) > > Regards, > > Edward > > > On Thu, Jan 8, 2009 at 12:16 AM, <[email protected]> wrote: >> Author: semor >> Date: Thu Jan 8 00:16:20 2009 >> New Revision: 8328 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=8328&view=rev >> Log: >> Moved the relax_time() function to cpmg_frq() and made other small changes. >> >> Still much (!) work is needed for this code to be complete. >> >> >> Modified: >> branches/relax_disp/specific_fns/relax_disp.py >> >> Modified: branches/relax_disp/specific_fns/relax_disp.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_disp.py?rev=8328&r1=8327&r2=8328&view=diff >> ============================================================================== >> --- branches/relax_disp/specific_fns/relax_disp.py (original) >> +++ branches/relax_disp/specific_fns/relax_disp.py Thu Jan 8 00:16:20 2009 >> @@ -168,6 +168,43 @@ >> return results[relax_time_index] >> >> >> + def cpmg_frq(self, frq=0, spectrum_id=None): >> + """Set the CPMG frequency associated with a given spectrum. >> + >> + @keyword frq: The frequency, in Hz, of the CPMG train. >> + @type frq: int >> + @keyword spectrum_id: The spectrum identification string. >> + @type spectrum_id: str >> + """ >> + >> + # Alias the current data pipe. >> + cdp = pipes.get_pipe() >> + >> + # Test if the spectrum id exists. >> + if spectrum_id not in cdp.spectrum_ids: >> + raise RelaxError, "The peak heights corresponding to spectrum >> id '%s' have not been loaded." % spectrum_id >> + >> + # Store the CPMG frequency in the class instance. >> + self.__cpmg_frq = int(frq) >> + >> + # The index. >> + index = cdp.spectrum_ids.index(spectrum_id) >> + >> + # Initialise the global CPMG frequency data structure if needed. >> + if not hasattr(cdp, 'frq'): >> + cdp.frq = [None] * len(cdp.spectrum_ids) >> + >> + # Index not present in the global CPMG frequency data structure. >> + while 1: >> + if index > len(cdp.frq) - 1: >> + cdp.frq.append(None) >> + else: >> + break >> + >> + # Add the frequency at the correct position. >> + cdp.frq[index] = frq >> + >> + >> def create_mc_data(self, spin_id): >> """Create the Monte Carlo peak intensity data. >> >> @@ -311,20 +348,25 @@ >> Relaxation curve fitting default values >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> - These values are completely arbitrary as peak heights (or volumes) >> are extremely variable >> - and the Rx value is a compensation for both the R1 and R2 values. >> - ___________________________________________________________________ >> - | | | | >> - | Data type | Object name | Value | >> - |________________________|_______________|________________________| >> - | | | | >> - | Relaxation rate | 'rx' | 8.0 | >> - | | | | >> - | Initial intensity | 'i0' | 10000.0 | >> - | | | | >> - | Intensity at infinity | 'iinf' | 0.0 | >> - | | | | >> - |________________________|_______________|________________________| >> + These values are arbitrary and will depend on the system studied. >> + >> ________________________________________________________________________________ >> + | | >> | | >> + | Data type | Object name >> | Value | >> + >> |___________________________________________________|_______________|__________| >> + | | >> | | >> + | Relaxation rate | 'R2' >> | 8.0 | >> + | | >> | | >> + | Chemical exchange contribution to 'R2' | 'Rex' >> | 2.0 | >> + | | >> | | >> + | Exchange rate | 'kex' >> | 10000.0 | >> + | | >> | | >> + | Relaxation rate for state A | 'R2A' >> | 0.0 | >> + | | >> | | >> + | Exchange rate from state A to state B | 'kA' >> | 10000.0 | >> + | | >> | | >> + | Chemical shift difference between states A and B | 'dw' >> | 100 | >> + | | >> | | >> + >> |___________________________________________________|_______________|__________| >> >> """ >> >> @@ -854,43 +896,6 @@ >> continue >> >> >> - def relax_time(self, time=0.0, spectrum_id=None): >> - """Set the relaxation time period associated with a given spectrum. >> - >> - @keyword time: The time, in seconds, of the relaxation >> period. >> - @type time: float >> - @keyword spectrum_id: The spectrum identification string. >> - @type spectrum_id: str >> - """ >> - >> - # Alias the current data pipe. >> - cdp = pipes.get_pipe() >> - >> - # Test if the spectrum id exists. >> - if spectrum_id not in cdp.spectrum_ids: >> - raise RelaxError, "The peak heights corresponding to spectrum >> id '%s' have not been loaded." % spectrum_id >> - >> - # Store the relaxation time in the class instance. >> - self.__relax_time = float(time) >> - >> - # The index. >> - index = cdp.spectrum_ids.index(spectrum_id) >> - >> - # Initialise the global relaxation time data structure if needed. >> - if not hasattr(cdp, 'relax_times'): >> - cdp.relax_times = [None] * len(cdp.spectrum_ids) >> - >> - # Index not present in the global relaxation time data structure. >> - while 1: >> - if index > len(cdp.relax_times) - 1: >> - cdp.relax_times.append(None) >> - else: >> - break >> - >> - # Add the time at the correct position. >> - cdp.relax_times[index] = time >> - >> - >> def return_data(self, spin): >> """Function for returning the peak intensity data structure. >> >> >> >> _______________________________________________ >> 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
