Hi, The original papers of Lipari and Szabo on model-free address the interpretation of relaxation data from methyl groups. I found no reference to the issue of the three reorienting CH vectors. It seems to me that the axis of symmetry of methyl rotation is used as a reference. Then, a Woessner model for the methyl motion is assumed, leading to a theoretical S2 of about 0.111 for methyl groups with perfect tetrahedral geometry. In this way one can obtain the S2 of the symmetry axis (eg. Ca-Cb vector in Alanine) by dividing the experimentally obtained S2 by 0.111. In any case, even with deuterium partial labeling you would have the proton jumping between positions meaning a time dependent vector orientation, no? I think the advantage of Deuterium is about the purity of the relaxation mechanism which is dominated by quadrupolar effects. Considering that I have acquired all the data in the absence of relaxation interference, is it feasible to use RELAX to fit the modelfree models? Regards Tiago Pais -----Original Message----- From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 12 de Agosto de 2009 15:07 To: Tiago Pais Cc: Vic Vostr; relax-users@xxxxxxx Subject: Re: value.display() Hi, Please see below for answers to your questions. On Wed, Aug 12, 2009 at 12:53 PM, Tiago Pais<tpais@xxxxxxxxxxx> wrote:
Dear Edward, I have some questions relating the functioning of relax 1.3.3: 1- When I initiate the relax command a get an error message about a
missing
DLL (python25.dll). However the program manages to start anf get to the command line. Is this DLL related to the "curve fitting" module? Does the relax program run properly without this DLL
This is a strange error. It is related to Python and not relax, and is the main Python library used by all Python programs. Do you have Python 2.5 installed? Could you cut and paste the error message? Do you get the same message if you run python from the command prompt as well?
2- The "relax --test-suite" routine seems to stall after a while. I have three "F" in the middle of the dotted line. Can this be related to the DLL
I'm not sure. If you're using Python 2.5 and getting this error, then relax should not run. This is strange. The stalling is likely to be on a system test which takes a while to run. It should be finished in 1-3 min though, unless you are using a very old machine. I'm currently fixing all the tests on windows in the 1.3 repository code, and relax 1.3.4 when released should pass most tests (note that 2 unit tests of the float module are know to fail).
3- The "TAB" button is not working within relax
This is a windows only problem as there is no special library called 'readline'. If this is too annoying, maybe running this in GNU/Linux (in a virtual machine if necessary) would be the easiest way to remove this lack of TAB key.
And now some question related to my specific case: 1- What is the nomenclature to describe the C nucleus in a methyl group? I will have to assume an effective CH vector and not three different ones
for
each proton; how do I tell this to the program?
This is slightly problematic because of all the cross-correlated relation rates (interference). There is no theory to handle this, that I am aware of. People overcome this by specific labelling so that there is one hydrogen and two deuteriums (e.g. see Lewis Kay's papers). Not only are the interference effects fatal, but the three CH vectors experience different spectral density functions J(w). The J(w) are direction dependent, and here you have three different directions which constantly change. Again the theory is completely missing, as far as I know. What you need is a reference where someone has handled the 1H-13C relaxation rates from a CH3 group before! Or you'll need to derive the necessary theory.
2- What is the format for the input R1,R2, and NOE data? Couldn't seem to find it written in the manual.
relax will handle any column formatted file. See the help for the relax_data.read() user function in the manual for full details, or type: relax> help(relax_data.read)
Sorry for all these questions but I am just starting dealing with this program.
No problems. If you have any other questions, please don't hesitate to ask. Regards, Edward