[phenixbb] sugar behaving sourly

Patrick Loll pat.loll at drexel.edu
Wed May 5 15:19:25 PDT 2010


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  

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  

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?


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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