Thank you, Edward! I have submitted a bug report #17458. I will check the updated version and get back to you if there are further problems.
Vitaly On Mon, Jan 10, 2011 at 08:49, Edward d'Auvergne <[email protected]> wrote: > Hi Vitaly, > > I've now fixed this bug in relax. It would still be useful to have a > bug report in case someone else encounters the same problem. As I > said in the commit message > (https://mail.gna.org/public/relax-commits/2011-01/msg00114.html), > this bug was recently introduced due to changes for BMRB support. It > affects relax 1.3.6, as well as the 1.3 line from revision r11678 to > r12174. As this bug is quite big affecting all users of model-free > analysis, I will try to release a new version of relax very soon. If > you have a repository version, you can type 'svn up' to receive the > bug fix. > > Cheers, > > Edward > > > > On 10 January 2011 11:00, Edward d'Auvergne <[email protected]> wrote: >> Hi, >> >> I can confirm a recently introduced bug in relax whereby the prolate >> tensor is actually oblate! I will try to solve this as soon as >> possible and release a new relax version. Strangely this was not >> caught by the relax test suite. But if you look in the prolate >> results file, you may see that the diffusion tensor is labelled as >> 'oblate'. Would you be able to submit a bug report for this? This >> will help other relax users who encounter the same problem. The >> submission form is located at >> https://gna.org/bugs/?func=additem&group=relax. >> >> Cheers, >> >> Edward >> >> >> On 6 January 2011 19:15, V.V. <[email protected]> wrote: >>> Ok, looks like "diff_min.py" is already setup to do everything I >>> wanted. :-) The problem with the prolate/oblate uncertainty still >>> exists though. I have a feeling that the constraint for Da=>0 or <=0 >>> is removed by the statement fix('diff', fixed=False). As a workaround >>> at the moment I use the following in the "diff_min.py": >>> >>> fix('diff', fixed=False) >>> cdp.diff_tensor.spheroid_type = 'prolate' >>> >>> This seems to do the trick. >>> >>> Vitaly >>> >>> >>> >>> >>> On Wed, Jan 5, 2011 at 16:14, V.V. <[email protected]> wrote: >>>> Hello, >>>> >>>> I am trying to optimize the diffusion tensor outside of >>>> "full_analysis.py", to avoid this prolate/oblate issue. I understand >>>> that the first round should be models tm0-tm9, followed by model >>>> selection, while the latter ones should alternate between the tensor >>>> optimization and model-free parameters fitting. I am not entirely sure >>>> how to start though. Should I: >>>> >>>> 1. Take the results from 'local_tm/aic', fix spins, initialize the >>>> diffusion tensor and then run grid search + minimization, then fix the >>>> tensor and optimize model-free parameters? >>>> >>>> or >>>> >>>> 2. Fix spins, initialize the diffusion tensor and perform m0-m9 runs >>>> followed by model selection, and after that fix the tensor and >>>> optimize MF? This seems to be what "diff_min.py" does. >>>> >>>> Thank you, >>>> Vitaly >>>> >>>> >>>> On Sat, Dec 18, 2010 at 23:25, V.V. <[email protected]> wrote: >>>>> Hello, >>>>> >>>>> I have performed a "full_analysis" run, and the Chi2 values for >>>>> prolate and oblate models were reported to be identical. I have >>>>> checked the contents of the /prolate/round_**/opt, and the results >>>>> file appears to contain the data for the oblate model: >>>>> >>>>> ================ >>>>> <diff_tensor desc="Diffusion tensor" type="spheroid"> >>>>> <Da ieee_754_byte_array="[144, 224, 168, 43, 17, 72, 82, 193]"> >>>>> -4792388.6821824461 >>>>> </Da> >>>>> <fixed> >>>>> False >>>>> </fixed> >>>>> <phi ieee_754_byte_array="[127, 197, 226, 164, 9, 205, 0, 64]"> >>>>> 2.1001160508828316 >>>>> </phi> >>>>> <spheroid_type> >>>>> 'oblate' >>>>> </spheroid_type> >>>>> <theta ieee_754_byte_array="[157, 42, 47, 69, 3, 109, 252, 63]"> >>>>> 1.7766144468793421 >>>>> </theta> >>>>> <tm ieee_754_byte_array="[131, 104, 243, 90, 176, 172, 60, 62]"> >>>>> 6.6763176508168525e-09 >>>>> </tm> >>>>> </diff_tensor> >>>>> ================ >>>>> >>>>> So, does it mean that the system is converging to the oblate model in >>>>> the prolate pipe? I thought the Da sign is constrained during the >>>>> search. >>>>> >>>>> Thank you, >>>>> Vitaly >>>>> >>>> >>> >>> _______________________________________________ >>> 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 >>> >> > _______________________________________________ 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
