[phenixbb] Composite omit map

[Dorothee Liebschner]

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 <samtys0910 at gmail.com> 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 <pafonine at 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
>>
>>
>
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