[phenixbb] maps : scattering corrections

Pavel Afonine pafonine at lbl.gov
Thu Oct 7 00:41:11 PDT 2010

  Hi Brian,

if you type


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.


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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> phenixbb at phenix-online.org
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