Hi Matt, Thanks for your reply. Following Bruce's instructions, I have re-compiled Ifeffit with a larger "max_restraint" number on a Linux Machine. It works fine. Now, I can compare fits obtained with a set of multiple restraints (more elegant) and with a combined (limited to 10) set of restraints. I did combine restraints before in the way almost as you suggested. Assuming that each restraint is squared before adding to chi-square, I used sum as follows restraint_sum = sqrt((restraint1)^2 + (restraint2)^2 + (restraint3)^2...) for group of similar atoms and bond lengths. I guess, the difference in sums should not have a significant effect on fit. However, the difference in fits with multiple and combined restraints is surprisingly noticeable. I expected that the mathematical distinction should be pretty small as you said. But it is not at least in this test. I should explore it a bit more. The restraints combined were for similar sets of both lengths in independent molecular units and should not be strongly anti-correlated. I wonder if when stereochemical restraint relations are used and a large number of independent not equally important (close to zero elements) restraints imposed, convergence and stability of minimization algorithm are affected by such a sparse normal-equations matrix. Regarding the examples with possible more than 10 restraints, I have a data for a solution of Cu(II)complex with two almost geometrically identical organic molecules. The crystal structure and total 28 bond distances with uncertainties are available in the literature. This amount can be reduced to 14 assuming 2-fold symmetry between molecules. I wanted to apply in XAFS fit bit more rigorous independent restraints using available from crystal structure bond distances with uncertainties. In addition, for proper sterochemical restraints (e.g. in "rigid-body" refinement) some bond angles and planar groups restraints may be required, which may be important for multiple scattering paths. I guess, to have a bit more flexibility in the amount of restraints (more than 10) can be useful when fitting data for bio-molecular systems. Victor Dr Victor Streltsov CSIRO Molecular & Health Technologies 343 Royal Parade Parkville VIC 3052 Australia Phone: +61 3 96627311 Fax: +61 3 96627101 victor.streltsov@csiro.au
Hi Victor,
As Bruce said, the limit of 10 restraints is compiled-in. It could certainly be increased.
But I'm impressed that you have more than 10 independent restraints to impose! Depending on the nature of your restraints, it might be possible to combine some of them. That is, using one restraint of
restraint_sum = (restraint1) + (restraint2) + (restraint3)
(where each restraint might be an elaborate calculation) is only different from using three restraints if the three restraints are strongly anti-correlated, so that they compete against one another. If you're restraining different bond lengths, some of them probably can be combined.
It's definitely better, and more elegant, to use multiple restraints, but I think the mathematical distinction may be pretty small.
--Matt