Hey all, let me give this discussion a little kick and see if it spins into outer space.
How many reflections do people use for cross-validation? Five per cent is a value that I read often in papers. Georg Zocher started with 5% but lowered that to 1.5% in the course of refinement. We've had problems with reviewers once complaining that the 0.3% of reflections we used were not enough. However, Axel Brünger's initial publication deems 1000 reflections sufficient, and that's exactly what 0.3% of reflections corresponded to in our data set. I would think the fewer observations are discarded, the better. Can one lower this number further by picking reflections smartly, eg. avoiding symmetry-related reflections as was discussed on the ccp4bb a little while back? Should one agonize at all, given that one should do a last run of refinement without any reflections excluded? Andreas On 1/31/07, Georg Zocher <[EMAIL PROTECTED]> wrote:
First of all, I would like to thank you for your comments. After consideration of all your comments, I conclude that there are three possibilities. 1.) search for some particularly poorly-behaved regions using parvati-server a.) refining the occupancy of that atoms and/or b.) tightening the restraints Problems which have already been metioned: If I tighten the restraints, the anisotropic model may not be statistically justified, which seems to be the case. Using all reflections may not help that much, because I chose a set of 1.5% for Rfree (~1300 reflections) to get as much data as possible for the refinement. For my first tries of anisotropic refinement I used 5% of the reflections for Rfree but the same problem arose, so that I decided to cut the Rfree to 1.5%. 2.) Using shelxl 3.) TLS with multi-groups Should be the safe way!? I will try all the possiblities, but especially the tls refinement seems to be a good option to be worthy to try. Thanks for your helpful advices, georg
