Pat Can you send me some of the inputs files directly. I'd like to see the restraints library and the .geo file. If you can send all the inputs and outputs it would be even better. Nigel On 5/5/10 3:19 PM, Patrick Loll wrote:
Hi,
I'm refining a structure with an unusual monosaccharide. I generated a library for this sugar from PRODRG, and it looks OK, at least to my eye. Certainly the obvious parameters like bond angle restraints seem normal.
However, when I refine with phenix, the sugar's C6 methyl group gets pushed out of density and assumes a very unnatural angle.
Now, it turns out that there are two copies of this molecule in the AU, and the other copy looks fine after refinement. Moreover, I can load my library into Coot, and when I use it to refine the sugar's position or regularize its geometry, it works just fine; and when I run phenix.pdbtools --geometry_regularization and supply my library, the resulting structure has nice geometry. These three observations lead me to believe that there's nothing inherently wrong with my library.
There are no steric clashes that would tend to push this methyl group out of whack (but just to be sure, I removed all nearby atoms and repeated the refinement, with the same result).
I should mention that this refinement is at ca. 1.8 Å, and the density for the sugar looks quite nice.
Any suggestions?
Cheers,
Pat Loll ---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA
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