Re: Addition of PDC support to relax 1.3.10 and an inconsistency in the error calculation.Re: Addition of PDC support to relax 1.3.10 and an inconsistency in the error calculation.|
Dear Edward, I quickly changed the code to vary the backcalculated y instead of the measured y to see which effect this has. Looking at the ratio errorFromRelax/errorFromPdc this gets sometimes closer but sometimes less close. How many MC simulations do you run and which variation do you use. I used 1000 runs and varied the values by adding gaussian noise, the width of the gaussian distribution identical to the integral error values as tabulated in the output file. Best regards, Peter On 2/24/2011 12:58 PM, Edward d'Auvergne wrote: Dear Peter, Cheers, I've added the new files to relax, and updated relax to handle them correctly. If there are any future changes, especially when the Dynamics Center comes out, I'd be happy to add support for these into relax. I hope that the Monte Carlo issue can be sorted out. It shouldn't take much to convert it from Bootstrapping, you just need to change the value which is being randomised from the measured value to the back-calculated value. Thanks for all your help. Regards, Edward On 24 February 2011 11:26, Dr. Klaus-Peter Neidig <peter.neidig@xxxxxxxxxxxxxxxxx> wrote:Dear Edward, I attached 3 files to the link (https://gna.org/task/?7180) you had sent me, it seems that everything worked. Regarding the T1, T2 files I added the columns you suggested and also supplied more digits. Please have a look a it. As you suggested most recently and as was also a result of some discussions here, we keep the confidence limit stuff since indeed other users not working in the area of relaxation data modelling have a different view on this. As I mentioned earlier the PDC will later become a part of a more general Dynamics Center (DC) that also offers T1, T2 etc but also for 1D data and small molecules and furthermore topics like kinetics, diffusion, Redor etc. The wish is here a uniform handling of all these methods. In the area of Export we have the option to become specific, adding Rx to an output that so far contained Tx for example is ok. Providing more details in the documentation is also no problem preferably by just giving references to books, papers or links. The Monte Carlo issue is still in discussion I do not expect a decision before the end of next week. If the basic stuff is sorted out we should at some time also compare our model-free analysis results. Of course there I expect differences since your implementations are much more advanced. Nevertheless the differences should be explainable and not too large. Best regards, Peter On 2/24/2011 10:32 AM, Edward d'Auvergne wrote: Dear Peter, Please see below: On 23 February 2011 19:33, Neidig, Klaus-Peter <Klaus-Peter.Neidig@xxxxxxxxxxxxxxxxx> wrote: Dear Edward, in short: the first 2 fit options (by fit, by weighted fit) both use the covariance technique. The difference is that the first option applies an additional internal scaling by: final chi/number of degrees of freedom This means that when doing modelling of (NOE, T1, T2) with (M1-M5, TM1-TM5) it cannot be used if these triples of number are only available at one field and the model contains 3 parameters. Could such details be given to the user? Many will know about the covariance matrix error estimation method (those that don't really should). But in in that area the PDC user does not have a selection of fit methods anyway, we internally use a combination of simplex and marquardt. But this is another area and should be done by relax anyway. For model-free, simplex is better than Marquardt. The problem with Levenberg-Marquardt is in the fine print. This method works well for most cases. But there is one situation where it totally fails, the fine print says that is when the internally used matrix is singular. At that point it cannot be inverted and the algorithm is forced to terminate. Unfortunately this happens a lot in model-free analysis, and it happens when a parameter is undefined. For example when S2 is perfectly 1 or 0. Then te can be anything - it falls out of the equations. This is the reason why there is much published data with order parameters of exactly 1. It is not because the residue is rigid, but because the optimisation came to a screaming halt. I pick up your statements about the confidence stuff. Indeed you are right that everything would be much simpler if the PDC did just output Rx instead of Tx and corresponding error. Whether keep the confidence stuff at all is then a question, in the mean I think I follow your opinion and would rather give it up. But this I have to discuss internally here. It might be that I'm not allowed to just give it up then I would have to increase the output with more columns or a further section which you could read instead of the current section. I think the confidence limit values have worth, some users will appreciated it. I would simply consider adding the additional information so that the user need not perform the conversion themselves. It would simply be an augmentation of the PDC output. There will be absolutely no new information in it as it is already in the file. I also have to say that my developments on the PDC must end by April (ENC) and this includes updating the manul, release procedure and some internal developments. So there is not too much time left. The PDC release number will then go up to 1.2. After April I can still maintenance work but no major changes, at least until someone decides something else. The simple solution would be some quick code adding a few columns. Additional columns should be no problem for parsers, as long as the original columns remain in place. The key for downstream analysis would be the R(1/2) value and standard deviation columns that the user can directly feed into the other software. Cheers, Edward . -- Dr. Klaus-Peter Neidig Software Development / Head of Analysis Group Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten, Germany Phone: +49 721 5161-6447 Fax: +49 721 5161-6480 Peter.Neidig@xxxxxxxxxxxxxxxxx www.bruker.com ________________________________ Bruker BioSpin GmbH: Sitz der Gesellschaft/Registered Office: Rheinstetten, HRB 102368 Amtsgericht Mannheim Geschäftsführer/Managing Directors: Jörg Laukien, Dr. Bernd Gewiese, Dr. Gerhard Roth Diese E-Mail und alle Anlagen können Betriebs- oder Geschäftsgeheimnisse, oder sonstige vertrauliche Informationen enthalten. Sollten Sie diese E-Mail irrtümlich erhalten haben, ist Ihnen eine Kenntnisnahme des Inhalts, eine Vervielfältigung oder Weitergabe der E-Mail und aller Anlagen ausdrücklich untersagt. Bitte benachrichtigen Sie den Absender und löschen/vernichten Sie die empfangene E-Mail und alle Anlagen. Vielen Dank. This message and any attachments may contain trade secrets or privileged, undisclosed or otherwise confidential information. If you have received this e-mail in error, you are hereby notified that any review, copying or distribution of it and its attachments is strictly prohibited. Please inform the sender immediately and delete/destroy the original message and any copies. Thank you.. --
| |||||||||