Re: [ccp4bb] Calculating ED Maps from structure factor files with no sigma
Hi Ed, I am not sure I understand this - perhaps we are talking about different things. Even if by inversion procedure you mean simple calculation of (2fo-fc)*exp(i*phi), the fc is still technically a product of the refinement, which unless based on trivial least square target (i.e. no weights) does factor in experimental errors. The (2mFo-DFc) map is even more obviously dependent on the errors. Again, I believe that the differences will be minor, but if one calculates a map with refmac either with or without factoring in experimental errors, there will be *some difference*. Thus, the experimental errors will affect the resulting map. Could you please clarify? Yes, we are talking about different things. I refer to the case that we have an amplitude term with its uncertainty (no matter whether it is Fo or Fo^2 or Fo-Fc or 2mFo-DFc or ...) plus a phase with its uncertainty. In normal everyday applications we use FFT which ignores (i) the uncertainties of both terms, (ii) the missing data. By doing an FFT we produce a map which exactly reproduces the input data (even if they are missing data which are reproduced with an amplitude of zero). What I have been saying is that in the presence of uncertainties and missing information the data do not define a single map, but a whole set of maps which are statistically consistent with the data and the question then arises : 'which map should I be looking at ?'. I happen to mention the maximum entropy method as a possible solution to this problem. I think that we are not comparing ML to no-ML (or maximum entropy), but rather ML inflated by experimental errors vs pure ML that ignores them. I may be crazy or stupid (or both), but certainly not crazy/stupid enough to doubt the importance of maximum likelihood for refinement. (On the other hand, one who promises to never doubt maximum likelihood shall never use SHELX :) We definitely talk about different things. My arguments had nothing to do with treatment of errors in refinement. The question I was tackling was how you go from |F|,sig(|F|),phase to a map in the presence of errors and missing data. Nicholas -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] Calculating ED Maps from structure factor files with no sigma
Hi Pete, I'm curious - which programs have you used for maximum-entropy for map calculation? Thanks, I thought no-one would ask :-) http://utopia.duth.gr/~glykos/graphent.html Don't download the program today. Or tomorrow. This coming weekend there will be a new release which will contain MacOSX executables. Nicholas -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] Refmac executables - win vs linux in RHEL VM
Hi Ian, Nicholas, this restriction applies (and has always applied) only to Intel's 'evaluation' licence That's right. With a cost of $9,997.00 for a 3-years/2-seats academic license, I couldn't have been talking for anything else ... :-))) All the best, Nicholas -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] Refmac executables - win vs linux in RHEL VM
Hi Ian, That sounds like way more than it should be, in fact it sounds like you've been quoted the cost of the commercial licence and then some! From Intel's website the academic licence for icc (Linux/2 seats) is $570 incl 1 year's support. Renewal of support for subsequent years will be less than this, probably around $250/year. I have ifort + icc (Linux/single user) we paid about $1200 for the 1st year, and $500 for subsequent year's support. The $9,997.00 price I quoted are for the XE parallel studio versions (C,C++,Fortran,...) as given at http://softwarestore.ispfulfillment.com/store/Product.aspx?skupart=I23S74 (which is where the page at http://software.intel.com/en-us/intel-sdp-home/ directs to if you select the C++ compiler for linux). For the XE version of C++ the prices for 3-year/2-seat academic is $6,499.00 (http://softwarestore.ispfulfillment.com/store/Product.aspx?skupart=I23S76) and for Fortran alone is $7,800.00 (http://softwarestore.ispfulfillment.com/store/Product.aspx?skupart=I23S91) I do not doubt that the prices you quote are also correct for a different product line (and I do not have anything against Intel :-) Nicholas -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
