Hi Edward,
>> But if [AMBER11] gives me de facto corrupted files I maybe just should use >> the >> attach_protons function of relax! > > Note these are not equivalent. The relax attach_protons function does > not create atomic coordinates for the new protons whereas AMBER's > does. This means that you cannot use it for the spheroidal or > ellipsoidal diffusion tensors in a model-free analysis. Oh, I didn't realize that. I just used the (corrupted) AMBER-generated PDB files which worked fine with relax 2. > You should > understand how AMBER places these protons and how other programs do > this too. I hope that one day relax will be able to do this, but that > will require a volunteer to add the algorithm. In case someone stumbles upon this thread in the future, there is documentation for the reduce function (http://kinemage.biochem.duke.edu/software/readme.reduce.html) which refers to the following publication: Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285: 1735–1747. http://www.pibs.duke.edu/downloads/PDFs/1999WordJMB285b.pdf >> Probably the conformational differences are too small to make a real >> difference in the subsequent MF analysis, given how large the actual errors >> of >> my rates etc actually are. I will look into this and if there's any >> difference, report back here. > > I unfortunately don't understand what this means. But if you mean > bond vector orientations, the relaxation rates are highly sensitive to > these even with low levels of anisotropy. To be honest, even I'm not understanding it. This was just a unqualified comment to reassure myself that something that looks so bad in the first place (a rather simplistic model of the spectral density function, a reduced set of parameters with huge errors, imperfect pulse programs, uncertainties in the X-ray structures and also the artificial addition of protons, and many variables I can't perfectly control) can yield interesting and reproducable data. You know, it's just the hope I will get some results I can work with. Cheers, Martin _______________________________________________ relax (http://www.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
