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

Oliver Clarke olibclarke at gmail.com
Tue Aug 16 10:06:58 PDT 2016

That makes perfect sense. Thanks for the quick and helpful reply Pavel.


On Tue, Aug 16, 2016 at 1:05 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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.
> Pavel
> 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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