[phenixbb] clashscore

Pavel Afonine pafonine at lbl.gov
Mon Nov 27 12:08:56 PST 2017

Hi Pan,

first off I suggest to inspect top worst clashes and see if they can be 
addressed. If that does not help, then try running several refinement 
runs each one using "nonbonded_weight" set to say 1000 (the default 
value), 5000, 10000, 25000, 50000. See how that changes the clashscore 
and model-to-map fit.

I would appreciate if you tell us what you find.

If you are using the command line then it is

phenix.real_space_refine model.pdb map.ccp4 resolution=3.1 

In the GUI:
Refinement Settings -> All parameters -> Search parameters : type into 
prompt nonbonded_weight, then OK -> In pop up prompt change 1000 to a 
desired value.


On 11/22/17 17:19, 潘 晓伟 wrote:
> Hello everyone
> I refine a cryo EM data with 3.1 angstrom, the model fit well with 
> the map, but the clashscore is high, abot 23.
> How can I decrease the value of clashscore with realspace.refinement 
> in Phenix GUI.
> Thanks!
> Pan

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