[phenixbb] rmsd: phenix vs refmac

Pavel Afonine pafonine at lbl.gov
Mon Dec 15 18:59:15 PST 2008

Hi Frank,

> But we're still seeing some much lower rmsd(bond) from phenix:  in 
> particular, when we take a refmac model and plug it straight into 
> phenix, the rmsd for cycle zero is already much lower than what it was 
> at the end of refmac.
> Could someone enlighten...?  (Yup, latest version of phenix.)

I have no idea about why they are different. I would approach this by 
taking a three-atoms test molecule, measure all bond lengths with a 
ruler (and calculate corresponding rmsd's) and then put this molecule 
into phenix.refine and refmac and see what they output.

Do you have such example?


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