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? On the other hand, phenix knows how to rotate a methyl group to avoid the H-H collision. -- Jianghai On Oct 29, 2010, at 5:42 PM, Nathaniel Echols wrote:

On Fri, Oct 29, 2010 at 2:01 PM, Jianghai Zhu wrote:

...

If I use the riding H atoms come out of phenix.refine in molprobity, it gives me a decent clash score. But if I strip the H atoms and let molprobity to add H atoms, I get a much worse clash score. I saw the manual of phenix recommends the first method. So what is the cause of the difference here? I know long time ago that phenix and molprobity used different bond length to add the riding H atoms. I don't know what the situation is now. Does phenix.refine refine the riding H atom positions?

It won't refine them against X-ray data, but it will perform geometry regularization to idealize their positions - which also includes shortening the bond lengths to match what we observe by X-ray diffraction. The program Reduce (used by Molprobity and Phenix), on the other hand, uses the nuclear distances, which I think are on average 0.1A longer. The Richardson lab is working on standardizing and reconciling the different bond lengths, but it's a messy problem (especially when neutron diffraction is involved).

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

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

Hi, I have a Cd(2)Cl(4)O(6) cluster in my structure and would like to set-up constraint files for it PHENIX. Any help here would be appreciated. O Cl Cl Cl O . . . . . . . . . . . . . . . . . O . . . Cd Cd . . . O . . . . . . . . . . . O Cl O Thanks, John John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077