Hi Markus,
I can only guess without seeing files (and link to files seems to be
broken).. So my guess is that the ligand density is weak enough so FEM
treats it as "near noise" and it wipes it. Polder decides it is likely
ligand because it uses correlations, and so even of two maps are weak but
similar the CC is going to be high. I can have a closer look if you send me
files (off mailing list!).
Pavel
On Fri, Nov 23, 2018 at 11:39 PM Markus Heckmann
wrote:
> Dear Pavel,
>
> By coincidence today I was looking at a soak-dataset and got totally
> confused with FEM (map) and Polder now.
>
> I am working on a dataset that processed it at 2.7A (in summer with
> XDS) and there was weak density for (OCA-Octanoic acid) when looked
> with FEM. This week, I retried it with DIALS and got about 2.6A (for
> CC_half 0.5). I ran FEM, and there was*no* density at all at OCA.
> After seeing this CCP4 answer, I ran Polder maps and it shows clear
> density for OCA. Now I am really confused why and what should I infer?
> Polder run also states "The polder map is likely to show the ligand."
> CC(1,2): 0.5639
> CC(1,3): 0.8722
> CC(2,3): 0.6193
>
>
> https://imagebin.ca/v/4NbuaSRUbc5t
> FEM in violet and Polder in Green
>
> Any guidance appreciated.
> Markus
>
>
>
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