Hi Ed, Thanks for the detailed and rapid answer !
These functionalities would be great ! The use of X-H vectors orientations spread could be used in cases where several structures are present to assess flexibility from different structures ! This would allow a better use of these structures, but also a better rationalization of NMR dynamics ! I propose these ideas could be added in the (already quite long) todo list... ;) As for what will soon be possible within relax, i.e. the possibility for the spin container to be filled with a list of orientations, how would you use relax to extract these orientations and output a list for each spin ? Is there a sample script for doing something like that ? This would be useful for someone interested in getting the orientations and analysing them out of relax, until the code is present... ;) Regards, Séb :) Edward d'Auvergne wrote: > Hi, > > I'm actually changing that code at the moment. If you follow my > commit messages you'll see how this will be handled in relax, very > soon. The changes are happening in the multi_structure branch where I > am introducing the distinction between different models (the same > molecules but with different conformations) verses different molecules > within one model. I'm modifying the structure.vectors() user function > now, and this is probably the one you are interested in. Using this > function, you can extract the vectors from all different models and > these will be placed in the spin container. With the 'ave' arg set to > False, each spin container will have a list of 3D vectors for all > models. > > As for analysing the spread of these vectors and then doing something > with that, nothing is present in relax. If you would like to have > this functionality, a little work will need to be done and a few > algorithms designed. The eliminate() user function for deselecting > spins is close but not quite what you need. It accepts an arbitrary > function but is not the correct place for this idea. Better would be > something like: > > deselect.mobile() > deselect.structural_noise() > deselect.vectors() > deselect.spread_vectors() > > with an argument such as (vector_spread_cutoff=0.53), where 0.53 is > some measure of the spread. This might be expandable to B-factors. > If the name deselect.mobile() is used, this could cover a vector > spread, B-factors, low S2 values, etc. Oh, with the deselect user > functions, there should always be a counterpart in the select user > function class. This will allow the deselected spins of the first > analysis to be used in a second with local tm values rather than a > global diffusion tensor. Is this what you had in mind? > > Regards, > > Edward > > > On Thu, Jan 15, 2009 at 4:33 PM, Sébastien Morin > <sebastien.mori...@ulaval.ca> wrote: > >> Hi, >> >> We are currently studying a system for which many structures are available. >> >> We thought it would be a great idea to compare X-H (N-H in our case) >> orientations to spot residues for which the orientation varies in the >> different structures, i.e. for which there might be important motions. >> >> We thought this could be useful to eliminate such residues with >> tremendous motions from diffusion tensor optimization and test them as >> diffusing independently (local tm). >> >> Is there a way to do that in relax ? >> >> We saw the sample script 'xh_vector_dist.py' which allows one to plot >> the vector orientations distribution. However, what we would like to get >> would be a file containing the orientations which could allow us to >> compare different structures quantitatively on a per residue basis... >> >> Thanks for help ! >> >> >> Sébastien Morin >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users mailing list >> relax-users@gna.org >> >> 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-users >> >> > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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-users
