[phenixbb] Meaning of "resolution" keyword for phenix.real_space_refine with mrc/ccp4 map input?

Pavel Afonine pafonine at lbl.gov
Tue Aug 16 10:05:45 PDT 2016

Hi Oliver,

it is only used to calculate correlation between experimental map and 
map calculated form the model (model-map CC). When you run 
phenix.real_space_refine you provide model and experimental map as 
inputs. To calculate model-map CC you need to calculate map from atomic 
model first. This is done by first calculating structure factors Fcalc 
from the model up to specified resolution and then FT'ing them into 
Fourier map that is then used to calculate CC.


On 8/16/16 09:59, Oliver Clarke wrote:
> Hi,
> What exactly does phenix.real_space_refine do with the mandatory 
> "resolution=" keyword when refining a model against a ccp4/mrc 
> formatted map?
> Is this purely for adjusting restraints etc, or does phenix internally 
> low-pass filter or resample the map based on this parameter?
> This seems like a basic question, so I apologize if the answer is 
> staring me in the face, but I couldn't see it in the online 
> documentation or in the output of phenix.real_space_refine --help.
> Cheers
> Oliver.

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