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 <pafonine@lbl.gov> wrote:
Hi Sam,

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