Re: [phenixbb] Weighting in phenix.real_space_refine

Hi Pavel, So how do I interpret the weights in the output? For example, with a structure I am refining at the moment, I have the following: "Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 0.0040 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 overall best weight: 9.4279” Is low tight and high loose, as for phenix.refine? And are there any prospects for the future of varying weights across the structure? Often in EM we will have large regions at good resolution, say <4Å, and other regions which while well defined are at lower resolution, say 6Å - applying the same weights to both regions doesn’t seem ideal. Would your suggested strategy at the moment be to split the structure domain-by-domain, refine domains separately and then recombine? Cheers, Oli (Also, there seems to be a very minor bug in the output model stats - “Dist moved from start” changes, but “Dist moved from previous” is always 0.000. Model statistics: Map CC (whole unit cell): 0.662 Map CC (around atoms): 0.773 rmsd (bonds): 0.01 rmsd (angles): 1.04 Dist. moved from start: 0.060 Dist. moved from previous: 0.000 All-atom clashscore 4.47 Ramachandran plot: outliers: 0.27 % allowed: 12.24 % favored: 87.49 % Rotamer outliers: 0.54 % C-beta deviations: 4)

On Sep 13, 2016, at 11:01 AM, Pavel Afonine wrote:

Hi Oliver,

...

So just to be sure - the average weight obtained with the randomly selected fragments is used for the entire model?

correct.

Pavel