[phenixbb] rmsd: phenix vs refmac - PS
pafonine at lbl.gov
Mon Dec 15 19:02:47 PST 2008
Also, can you get Refmac output all target values (ideal bond lengths,
etc) used in restraints calculation? phenix.refine outputs a complete
picture of restraints used (see .geo file). Is there anything similar in
Refmac? If there is, then you could compare the values atom by atom.
On 12/15/2008 6:59 PM, Pavel Afonine wrote:
> 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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