Re: [phenixbb] Riding H

As I said, stripping the H and re-add the H has a little problem. Because the methyl group can rotate, phenix.refine actually rotates the H atoms on the methyl group, a lot of clashes can be avoided. While the molprobity and phenix validation tools can't do that, a lot more clashes appear. -- Jianghai On Oct 29, 2010, at 6:35 PM, Nathaniel Echols wrote:

On Fri, Oct 29, 2010 at 2:56 PM, Jianghai Zhu wrote:

...

That is what I thought. But wouldn't the nuclear distance be more accurate? and we should use the molprobity bond length, the longer one?

I'm not sure what is most accurate from the standpoint of a molecular modeler or chemist, but as far as X-ray diffraction is concerned, the shorter distance is better - however, the difference in R-factors is minimal, even at atomic resolution. Internally, we're using the same monomer library that Refmac uses, so it's non-trivial to switch to the longer distances. I suspect it might improve the geometry, but I haven't tested this.

For what it's worth, the validation tools in PHENIX (which includes most of Molprobity at this point) always strip and re-add hydrogens before calculating clashes, so the result will always reflect the longer bonds.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb