That is extremely useful information, thanks! Jeremy Anderson
Ph.D. Candidate Johns Hopkins University Program in Molecular Biophysics Laboratory of Dr. Vincent J. Hilser, Ph.D. 3400 N Charles St, 104 Mudd Hall Baltimore, MD 21218 (Lab) *410-516-6757* (Cell) 715-613-0274 On Tue, Nov 15, 2016 at 8:49 AM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > On 15 November 2016 at 14:33, Jeremy Anderson <jande...@jhu.edu> wrote: > > Hi Edward, > > > > Thanks for the follow up. I totally understand the reasons for not > having > > fixed values within a relax analysis, it seems like a special case > relative > > to what I've seen in the literature and increases ones ability to skew > the > > results to their liking, I'm doing my best to safeguard against that > myself. > > No problems. You do have to be quite careful, as it is far too easy > to fall into an alternative reality that can nicely explain some of > the biology. Mapping the optimisation space is an essential tool when > constraining certain parameters to see if you are at a well defined > minimum. For example it can show you if you've just chopped across a > valley in the space and the optimiser is landing at the bottom of that > valley where it has been cut. If you have access to the ancient, yet > very powerful OpenDX software, you can use the dx.map and dx.execute > relax user functions for this. > > > > I was able to implement such an analysis in python using the RD models > from > > relax as well as the scipy and lmfit packages to both hold the dw > parameters > > constant while performing the usual grid search then nonlinear least > squares > > minimization and perform a cluster analysis holding the rate constant > and/or > > the major population constant amongst all residues. The code is a bit > of a > > mess at the moment but I'm hoping to clean it up and make a repository on > > github, so I can better document what I did and so other folks can check > it > > out if they want. > > Note that I originally looked at the scipy optimisation packages for > relax. However I found fatal bugs in all three of the algorithms > implemented at the time (Levenberg-Marquardt being one of them). The > algorithms appeared to minimise the results, but they were nothing > like what Art Palmer's Modelfree4 found. I was comparing relax to > Modelfree4 for debugging at the time when implementing the model-free > analysis component. I don't know if anything has changed since then, > but you really need to be wary and double check whenever you use any > part of scipy. Anyway, because scipy's optimisation was so terrible, > I decided to write the minfx optimisation library > (https://gna.org/projects/minfx/). You'll see a record of all of this > in my publication history ;) > > > > Thanks for your assistance. > > You're welcome! > > Regards, > > Edward > _______________________________________________ relax (http://www.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
