Dear Ian, On Fri, Sep 12, 2008 at 05:53:35PM +0100, Ian Tickle wrote: > > I would have thought that it would always be a good idea to refine only > the occupancies in the first few cycles and only refine co-ords & B > factors once the occupancies have settled down to sensible values.
Correct, this is exactly what SHARP/autoSHARP does by default: refining occupancies and scale factors (including non-isomorphism parameters) first, then adding coordinates and finally B-factors. > But in that case wouldn't the Fcalc's be linearly dependent on the > occupancies so the occupancy-only refinement should be reasonably > well-behaved, even from a distant starting point? The initial > guesstimates of the occupancies could be significantly off even if > the data is correctly scaled so the refinement still needs to be > reasonably robust. It all depends how far away 'distant' really is I guess. Imagine a case where you only have poor 4A data, with a possibility of 6-24 mol/asu (ok, at that resolution a low number is more likely), you found two heavy atom positions of a soak (so no idea about real occupancy anyway), have no idea about B-factor (100? 200?) for these heavy atoms and you want to phase using SIRAS with a fairly non-isomorphous native (2A cell shift) to go with the derivative (that is only 85% complete). And for good measure you had severe radiation damage and highly anisotropic diffraction of a split crystal. Unfortunately this doesn't sound too unlikely to me I must say ... seen a few of those cases that shout "Grow better crystals!". But the poor scientist is desperate to finish the thesis/project on time because the PI/boss/patent lawer is pressuring and the next position/job/Nobel prize is already sorted ... and the competition is starting writing up ... etc. In such a case you have to try to eliminate as much uncertainty as possible. And having the data on a roughly absolute scale (still a factor of 10 or more off is fine) might help - even if it only gives you the positive feeling that at least that part of a difficult project was dealt with correctly ;-) > But I agree with you, there can't be any harm in applying the Wilson > scale factor, so you may as well always do it, at least it ensures that > the range of values for the F's is roughly right (and you're less likely > to get questions like "why are my occupancies more than 1 ?"!). Another argument is that if people write ASCII files containing intensities/Fs the values will fit into the particular format (one of the advantages of a binary format like MTZ: you're unlikely to loose accuracy by hitting some arbitrary printf/write statement). Cheers Clemens -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
