[phenixbb] maps : scattering corrections
Pavel Afonine
pafonine at lbl.gov
Thu Oct 7 00:41:11 PDT 2010
Hi Brian,
if you type
phenix.maps
and hit return
it will print out some on-screen information about the program, ahat it
can do and how, and it will created a parameter file ot compute the maps
(maps.params). You can edit that file to customize your maps, and then
run it as
phenix.maps maps.params
Yos you can see the "anomalous_scatterers { " is not mentionaed anywhere
in that parameter file maps.params, obviously meaning that these
parameters cannot be defined for phenix.maps. (you probably confuse it
with phenix.refine where you can do it.)
If you tell me what exactly you are trying to achieve then I will try to
help with existing tool or I will add new functionality so you can do
what you want. Well, I guess I have an idea, so I will work on this as
soon as I get a chance.
Pavel.
On 10/6/10 12:21 PM, Lepore, Bryan wrote:
> i'd like to define anomalous scattering corrections for phenix.maps, it looks like i'm not doing it right.
>
> it appears that simply pasting in various adjustments of :
>
> anomalous_scatterers {
> group {
> selection = element = Ni
> f_prime = 2.4
> f_double_prime = -0.1
> refine = *f_prime *f_double_prime # not sure about this one
> }
>
>
> in various places in maps.params mostly causes phenix.maps to report "unused parameter", e.g:
>
> maps.anomalous_scatterers.group.selection
>
> this should work, right? what am i missing here - is there a scope missing, what scope does this go in, did i miss this in the docs...
>
> -bryan
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