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[ccp4bb]: defining sugar connectivity in refmac5



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hello,

I'm using refmac5 for the refinement of a glycoprotein, and I have some
problems with my sugar links definition. Although the sugar bonds are
correctly found by refmac5 from the coordinates, the resulting model
does not reflect those bonds (even in IDEALISE mode).

In refmac5 command file, I'm using :
MAKE HYDR ALL
MAKE CHECK ALL
MAKE BUILD NO
MAKE LINK YES
MAKE SUGAR YES

The logfile states that the following sugar links were identified :
  WARNING : link:NAG-ASN  is found dist =     1.428 ideal_dist=    
1.439
            ch:AA res:  71  ASN      at:ND2 .->BB res:   1  NAG     
at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.413 ideal_dist=    
1.439
            ch:BB res:   1  NAG      at:O4  .->Ba res:   2  NAG     
at:C1  .
  WARNING : link:BETA1-3  is found dist =     1.468 ideal_dist=    
1.439
            ch:BB res:   1  NAG      at:O3  .->Bd res:   3  FUC     
at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.413 ideal_dist=    
1.439
            ch:Ba res:   2  NAG      at:O4  .->Bb res:   5  MAN     
at:C1  .
  WARNING : link:ALPHA1-6 is found dist =     1.443 ideal_dist=    
1.439
            ch:Bb res:   5  MAN      at:O6  .->Bc res:   6  MAN     
at:C1  .
  WARNING : link:BETA1-2  is found dist =     1.455 ideal_dist=    
1.439
            ch:Bb res:   5  MAN      at:O2  .->Be res:   7  XYS     
at:C1  .
and they should be used for refinement.

In the resulting model (IDEALISE and REST mode), I have unrealistic
distance :
NAG 1B O3 - FUC 3B C1 : 3.8 A instead of 1.439 A (BETA1-3 above)
MAN 5B O2 - XYS 7B C1 : 3.3 A instead of 1.439 A (BETA1-2 above)
Both links were identified in the list above.
Other sugar links seem correct.

It looks as if the covalent bonds is not restrained, and only a VdW term
is used instead.

Any ideas what might be wrong ?

Thanks a lot for your help

laurent
-- 
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Laurent Maveyraud                  mailto:laurent.maveyraud@ipbs.fr
I.P.B.S. UMR 5089                 Groupe de Biophysique Structurale
Département Mécanismes Moléculaires des Infections Mycobactériennes
205 route de Narbonne                   31077 TOULOUSE Cedex FRANCE
Tél: +33 (0)561 175 435                    Fax : +33 (0)561 175 994
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