PS. 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. Pavel. 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?
Pavel.