[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[ccp4bb]: defining sugar connectivity in refmac5 (addendum)
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Dear all,
since my previous email, I noticed as well that the two problematic
sugar links (BETA1-3 and BETA1-2) were not written in the formatted
restraints file that refmac5 writes when requested to, although the
logfile claims they were correctly identified.
Maybe this will help to locate the problem...
I tried Eleanor's suggestion (thank you, Eleanor), but the problem
persists.
thanks for your help
laurent
here his my orignial message :
> 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.
--
-------------------------------------------------------------------
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
-------------------------------------------------------------------