[phenixbb] sugar behaving sourly

Nigel W Moriarty NWMoriarty at lbl.gov
Wed May 5 15:33:07 PDT 2010


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.


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
> (215) 762-7706
> pat.loll at drexelmed.edu
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909     Web   : CCI.LBL.gov

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