Re: [phenixbb] Composite omit map

Hi Sam, The correlation coefficients look rather poor. However, the most important is to inspect the maps. But, i the maps do not show evidence of the nucleotides, it is difficult to "prove" that they are there (or have a particular orientation). To get clues from the map, I would f.ex. look for a higher peak which could indicate the P position. Also, as it was suggested in the other thread, build/improve as much of the model as you can, and then investigate details. You can read more about the Discrepancy function D in: Urzhumtsev, A., Afonine, P. V., Lunin, V. Y., Terwilliger, T. C. & Adams, P. D. Metrics for comparison of crystallographic maps. *Acta Crystallogr. Sect. D Biol. Crystallogr.* *70,* 2593–2606 (2014). http://scripts.iucr.org/cgi-bin/paper?kw5094 Best wishes, Dorothee On Mon, Jun 5, 2017 at 7:43 AM, Sam Tang wrote:

Hi Pavel

Thanks again for the advice. I have run Polder map on two of the nucleotides in doubt. The CC for one of them: N1:CC(1,2): 0.5610 CC(1,3): 0.6212 CC(2,3): 0.5193

Peak CC: CC(1,2): 0.5444 CC(1,3): 0.5798 CC(2,3): 0.4921

The embarrassing issue here is that these two nucleotides make complete sense biologically if they turn out to be flexible. Will the high B-factor hinders the calculation of CC in Polder map? Meanwhile, I notice there is a column labeled 'q' in the log output like the below

q D(1,2) D(1,3) D(2,3) 0.10 0.4162 0.7689 0.6533 0.20 0.4748 0.6926 0.6796 0.30 0.5252 0.6516 0.6466 0.40 0.6243 0.6590 0.6937 0.50 0.6576 0.6160 0.7034 0.60 0.6851 0.5420 0.6807 0.70 0.7606 0.5029 0.6442 0.80 0.8422 0.4325 0.6959 0.90 0.9365 0.4567 0.7226 0.91 0.9783 0.4447 0.7750 0.92 0.9614 0.4666 0.7352 0.93 0.9591 0.4955 0.7513 0.94 0.9594 0.5258 0.8026 0.95 0.9639 0.5805 0.7558 0.96 1.0026 0.6504 0.8130 0.97 0.9655 0.6079 0.7867 0.98 1.0087 0.9025 0.8495 0.99 0.8934 0.9460 0.8934

Could you enlighten me as to the meaning of these or where I could go for relevant readings?

Many thanks indeed.

Kind regards

Sam

On 4 June 2017 at 11:23, Pavel Afonine wrote:

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Hi Sam,

I have tried Polder Map as well as the conventional SA-OMIT map. My

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feeling is that the conventional way gives better map for the ligand at the 'good' region than Polder, but neither way improves density at the 'poor' region.

I'd say it's more about getting convincing map rather than (artistically) looking better one. If three CC numbers that Polder map tool reports are in favor of the ligand then this is what you've got. By design, any sort of OMIT map is expected to appear worse than say usual 2mFo-DFc map (it is naive to expect that by removing bits of model you get a better looking map).

Both methods you quote are to show you the map, not to improve the model so that in turn you get an improved map.

Pavel

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