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*To*: ccp4bb@dl.ac.uk*Subject*: Re: refmac for partial p-ala trace / refinements*From*: Alexandre Urzhumtsev/Ourjoumtsev <sacha@lcm3b.u-nancy.fr>*Date*: Wed, 12 Jan 2000 11:03:11 +0100*Sender*: owner-ccp4bb@dl.ac.uk

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html *** Hi, again, as for a number of previuos cases, I would agree with Dirk's Kostrewa comments and would even emphasise his scepticism. I think it is worthy to understand what you are doing when you are solving a structure and I would like to give some comments for young researchers. There are no miracles, specially in optimisation procedures - refinement is a praticular case of it. As in any optimisation, you have : a) a criterion to be optimised and b) the procedure to search for the (GLOBAL) minimum - if we believe that this minimum corresponds to the right model. There is NO method for global minimum search for an ARBITRARY function (except a systematic checking of its values for ALL possible values of its argument). Crystallographers use now a mixture of random methods with local minimisation (gradient based) which work in general well for OUR PARTICULAR PROBLEMS but they CANNOT garatee to find a global minimum when starting from a quite wrong (or POOR !! or INCOMPLETE !!) model. But - we do not have a better procedure for a time being. ML is a minimisation CRITERION, and NOT a minimisation method. One can compare it with the least-square criterion. It works in the same way except that instead of fitting calculated magnitudes to the observed one it suggests to fit them to some MODIFIED VALUES, and these modifications are extimated through the model quality and completeness (see, for example, explanations in the last issue of the CCP4 Newsletters). If the model is incomplete, it is wrong to fit it to experimental amplitudes (as it is the case in the LS refinement) and ML knows how to introduce such corrections. Such corrections are done in resolution shells. If your model does not fit at all your data at a given resolution shell, the ML puts the "corrected experimental magnitudes" in this shell equal to zero. IF in this case they still participate in optimisation, this is even dangerous to use these reflections. IF in this case they are simply removed from the refinement procedure, this means exactly "old good scheme" of refinement when one increases the resolution slowly. (I do not know exactly which of these alternatives is programmed.) Including of all data is good when your have a high-resolution data set (which rather mean that your crystal is good, your density is good, and your model is supposed to be quite good and complete originally - without or with some dummy-atoms as it in ARP). Best regards, Sasha

**Follow-Ups**:**Re: refmac for partial p-ala trace / refinements***From:*Johan Turkenburg <jpt@ysbl.york.ac.uk>

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