Hi, I've been thinking about the options for this, and think that you have covered all the standard relaxation rates for a two spin system. I just wonder, how do you identify which nucleus type, 1H, 13C, 15N, etc. matches the I or S nominclature? And how does this apply to the situation where you have collected C and N relaxation rates for the same residue (backbone amide N and Ca, or RNA relaxation rates)? Would these be stored in different saveframes? Also, it's very important to know the labelling state, i.e. is it double labelled with 15N and 13C, is it deuterated, etc. This would already be within the NMR-STAR definition, would it not? Oh, also is there a reason for the brackets in I(+,-)? The + and - are not usually used with brackets, but are placed as superscript.
As for the saveframe label, could it be something like 'relaxation_data' or 'relaxation_rate'? Could it be extended to include the R1, R2, and R1rho as possibilities so that the saveframe covers all standard relaxation rates of a 2 spin system? This would make the Heteronucl_T*_list frames redundant but might make future parsing by external programs simpler. One important part missing from all of this is the relaxation rates that TROSY, CRIPT, CRINEPT, etc. depend upon. There is no option for storing cross-correlated relaxation (also know as relaxation interference). Most rates measured are the cross-correlation between the CSA relaxation and the dipolar relaxation of a heteronuclear 2 spin system. But you can also have cross-correlation between 2 or more dipolar relaxation mechanisms, for example in a methyl group. An important use for this in relaxation analyses is that for big systems, RNA, etc., the cross-correlated rates eta_z and eta_xy can be used as replacements for the R1 and R2 rates respectively. This is not yet in relax, but wouldn't take me very long to add once someone with these rates would like to perform model-free or another analysis. One possibility would be to use operators such as I(+,-)Sa, I(+,-)Sb, IaS(+,-), IbS(+,-). I'm not sure of all the possible options here, but the eta rates may not be able to be split into these 4 components in all cases. And then for a full listing of these rates, again I'm not sure of all the possibilities. Regards, Edward On Sat, Jan 24, 2009 at 6:40 PM, Eldon Ulrich <[email protected]> wrote: > Hi, > > For the T1(R1), T2 (R2), and T1rho (R1rho) relaxation data a tag has been > available in the NMR-STAR dictionary for defining the 'coherence type' that > was observed in collecting the data. It has been pointed out that the > enumerated values for the coherence type tags were not accurate. The > existing enumerations include atom types (N, H, etc.), information repeated > in some sense in the data tables where the atoms involved in the relaxation > are listed. > > In trying to improve how these data are represented, we have consulted with > people in the NMR facility here and have derived the draft proposal shown > below and would like to have feed back from you and those working on the > Relax project. > > In this proposal, I and S are used as the general terms for the spins > involved. 'z' and '+' and '-' are used to describe the magnetization. In > addition to the tables for T1, T2, and T1rho, a new saveframe > (general_relaxation) has been added to capture relaxation data that may not > fit in the other categories. If a better term than 'general_relaxation' > would fit these kinds of data, please provide your advice. > > Your comments and suggestions would be very helpful. > > Thank you, > Eldon > > save__Heteronucl_T1_list.T1_coherence_type > > loop_ > _item_enumeration_value > _item_enumeration_description > > Iz 'zero quantum, longitudinal' > Sz 'zero quantum, longitudinal' > > stop_ > > save_ > > > save__Heteronucl_T1rho_list.T1rho_coherence_type > > loop_ > _item_enumeration_value > _item_enumeration_description > > I(+,-) 'single quantum' > S(+,-) 'single quantum' > > stop_ > > save_ > > save__Heteronucl_T2_list.T2_coherence_type > > loop_ > _item_enumeration_value > _item_enumeration_description > > > I(+,-) 'single quantum' > S(+,-) 'single quantum' > > stop_ > > save_ > > save__General_relaxation_list.Relaxation_coherence_type > > loop_ > _item_enumeration_value > _item_enumeration_description > > I(+,-)S(-,+) 'zero quantum' > IzSz 'zero quantum, longitudinal spin order' > I(+,-)Sz 'single quantum, antiphase' > IzS(+,-) 'single quantum, antiphase' > I(+,-)S(+,-) 'double quantum' > > stop_ > > save_ > > > > > > _______________________________________________ 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
