Hi Edward, So I've got wild type = oblate chosen, and mutant = ellipsoid chosen. When you look at the wild type, this gets the strange low values in both oblate and ellipsoid, but not prolate/sphere. The mutant has beautiful values in all. I'm wondering whether the wild type data is just not as good. I might need to go over it - I did it much earlier, so my peak picking might be wrong. I've found that R1 and NOE values agree very well, as they should, but R2 are very different - since these experiments have the largest noise, it may be due to the way I peak picked them - with the mutant I actually manually peak picked, whereas with the wild type I didn't I just picked every peak on the same spot, using the peak in the first delay as a reference. I think the latter technique may help with the R2 values. Chemical exchange should be similar in both apart from the mutated loop, where it disappears in the mutant.
I think basically - the two proteins where I manually peak picked I got the best results, and in the fastest time too, with the fewest rounds. The two proteins where I didn't worry as much about the T2 data, I got extremely long calculation times and I ended up having to delete some residues' data in order to allow the programme to finish. I think it might be best if I go back and look at the T2 data again and rerun for the latter two proteins. Maddy ---------------------------- Original Message ---------------------------- Subject: Re: [Fwd: Re: Extracting results - eg sphere] From: "Edward d'Auvergne" <[email protected]> Date: Thu, June 16, 2011 8:10 am To: "Maddy Strickland" <[email protected]> Cc: [email protected] -------------------------------------------------------------------------- Hi, It is strange that the S2 values are so far off. Are they the same if you look at both ellipsoids or both prolate spheroids? How do the diffusion tensors compare? Did you use single-scan interleaving, temperature compensation blocks, and per experiment MeOH temperature calibration? Do you see extensive chemical exchange or nanosecond motions? How did you use relax, and which version of relax are you using? How do both sets of NOEs compare, is the average identical in both systems? And are the R1 and R2 averages the same? For the global models that are not in the 'final' run, it is true that these have no errors. The reason is that Monte Carlo simulations are expensive, computationally wise, so they are only used at the very end once all model selection is performed. You can use relax to calculate the errors for each model anyway. If you go to the last round_*/opt directory, you can use a custom script there. Try something like: # Load the program state. state.load('state') # Monte Carlo simulations. monte_carlo.setup(number=500) monte_carlo.create_data() monte_carlo.initial_values() minimise('newton') eliminate() monte_carlo.error_analysis() # Save the program state. state.save('state_errors', force=True) You will have to play with this, as you might have to fix the diffusion tensor if calculations are far too long. Or there might be other option you'll need to play with too, but hopefully together with the relax manual that shouldn't be too hard to work out. Regards, Edward On 15 June 2011 15:06, Maddy Strickland <[email protected]> wrote: > Yes, I want to look at all the different models - sphere/ellipsoid/prolate > etc. to see how S2 values differ. I've got two proteins - one of which is > a mutant of another (only a few residues mutated), but they came out with > different models, one with ellipsoid and one with prolate. When I > compared the S2 values for the two, one was about 0.5 different on every > value (the prolate model was completely off). When looking at the > spherical model it is much closer to what is expected. (I have four > homologous proteins and all are very similar except this prolate model, so > I can't work out why this is so different and I can't work out why it has > been chosen with such strange S2 values. I wanted to compare all four > spherical models instead of using anisotropic ones. I have worked out how > to do this, but unfortunately, I think S2 error and Rex error is > calculated right at the end in the 'final' round as I can't seem to > extract this from 'opt' folders in the final round of 'sphere' or > 'prolate' for example. > > Any ideas? Is error calculated in each round, or is it calculated right > at the end and therefore impossible to collect for individual > 'sphere'/'prolate' etc. that haven't been chosen? > > Maddy > > ---------------------------- Original Message ---------------------------- > Subject: Re: Extracting results - eg sphere > From: "Edward d'Auvergne" <[email protected]> > Date: Tue, June 14, 2011 10:17 am > To: "Maddy Strickland" <[email protected]> > "Michael Bieri" <[email protected]> > Cc: [email protected] > -------------------------------------------------------------------------- > > Hi Maddy, > > It should be possible, but you may have to manually modify your > extraction scripts. All of the results files are saved, so all of the > data is there. I'm assuming you'd like to compare the different > diffusion tensor results, is that correct? You will need to choose > which file you look at. Just look through the directories and pick > the final round for each tensor, and go into the 'opt' directory. The > results.bz2 file in that directory will be the one you want. Maybe > Michael can help with the modification of his script, if you are > having troubles. > > Regards, > > Edward > > > > On 9 June 2011 13:03, Maddy Strickland <[email protected]> wrote: >> Hello everyone, >> >> I was wondering if there was a way to extract results, say just from the >> spherical folder or just from the ellipsoid folder for example, displayed >> as s2.txt, rex.txt etc. like with the final data extraction script, but >> for a different model than is selected by the program? >> >> >> Madeleine Strickland >> >> MCJC Group >> N317, School of Chemistry, Bristol University >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users 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-users >> > > > Madeleine Strickland > > MCJC Group > N317, School of Chemistry, Bristol University > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users 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-users > Madeleine Strickland MCJC Group N317, School of Chemistry, Bristol University _______________________________________________ relax (http://nmr-relax.com) This is the relax-users 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-users
