Hello,

Have you tried ISOLDE? Interactive MDFF is really powerful both for fixing 
models with poor geometry and for improving fit to the map.

There is a good tutorial for refinement of a model against a cryoEM map with 
ISOLDE: 
https://isolde.cimr.cam.ac.uk/static/isolde/doc/tutorials/intro/cryo_intro/cryo_intro.html

I hope this helps,

Guillaume

> On 29 Jul 2020, at 17:29, Schreuder, Herman /DE <herman.schreu...@sanofi.com> 
> wrote:
> 
> 
> Coot does it, but if one wants to do it for a complete protein, it is a lot 
> of clicking. On the other hand, I have not tried to just select the N- and 
> C-terminus for real-space refinement to see what happens. I would prefer to 
> have some script to do it.
> Best, Herman
>  
> Von: Eleanor Dodson <eleanor.dod...@york.ac.uk> 
> Gesendet: Mittwoch, 29. Juli 2020 17:23
> An: Schreuder, Herman /DE <herman.schreu...@sanofi.com>
> Cc: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
>  
> EXTERNAL : Real sender is eleanor.dod...@york.ac.uk
> 
>  
> 
> Wont coot do that?
> Eleanor
>  
> On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE 
> <herman.schreu...@sanofi.com> wrote:
> Dear BB,
>  
> I would like to do a real real-space-refinement of a protein against a 
> cryo-EM map; not the mtz-based Refmac approach. A quick internet search 
> produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how 
> to do this using ccp4 programs, or has someone a Coot script to do this?
>  
> Thank you for your help!
> Herman
>  
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