perhaps there still is a problem with refmac

from the iupac carbohydrate pages
http://www.chem.qmul.ac.uk/iupac/2carb/06n07.html
see section 2-Carb-7.4. Enantiomers

if a sugar has a configuration in a chair form for
a trans 1--6 then it will be trans-like in both alpha-L and alpha-D

 1C4 to 4C1 but both are axial -O1

see the example above url
á-D-glucopyranose-4C1  and á-L-glucopyranose-1C4

the 1,2-torsion changes stays cis or trans depending
on the actual sugar

changing a 1,6, a five bond connectivity is not possible
the orientations stay the same

in plane project for alpha-fucose
 L has O1 O2 up   O3 O4 C5 down
 D has O1 O2 down O3 O4 C5 up
  no change in any cis or trans torsions

in the PDB
a-D-FUC is 3-letter code FCA
a-L-FUC is 3-letter code FUC

you can get the ideal coordinates fro FUC and FCA from either the
http://www.ebi.ac.uk/msd-srv/msdchem/
or the wwpdb
http://remediation.wwpdb.org/downloads.html
and the dictionaries from G.K.
http://alpha2.bmc.uu.se/hicup/

alpha and beta change torsion angles from cis/trans



> Sorry guys,
>
> my previous message obviously reflected that I am not very familiar with
> sugars. Kelvin's email clarified what was going on: the REFMAC dictionary
> for a-L-fucose is perfectly correct, my mistake was that I was not aware
> of the reverse relation of alpha and beta-linkages in L and D-sugars!
>
> Thanks again for the clarification, and sorry for bugging you all,
>
> the sugar-greenhorn Petra
>
>
>
> ---------------------------- Original Message ----------------------------
> Subject: Re: [ccp4bb] REFMAC converts alpha-L-fucose into beta-L-fucose
> From:    "Kelvin Luther" <[log in to unmask]>
> Date:    Wed, June 13, 2007 5:00 pm
> To:      [log in to unmask]
> --------------------------------------------------------------------------
>
> I just wanted to mention something in case you're not familiar with
> sugars.  Alpha and Beta for an L sugar will be reverse of alpha and beta
> for a D sugar.  Alpha for a D-sugar is when the c6 constituent and the
> anomeric carbon constituent are in opposite orientations.  With fucose,
> an L sugar, such a configuration would be beta.  Hope this is the
> problem, in which case, there isn't one.
>
> Cheers,this
>
> Kelvin Luther
>
> On Wed, 13 Jun 2007, [log in to unmask] wrote:
>
>> Dear CCP4bb
>>
>> thanks so much for the helpful information regarding carbohydrate
> refinement. Kim's recommendation (see below) for the validation server
> worked really well and helped me to finally figure out what is going on.
> Seems as if REFMAC5 (part of ccp4-6.0.2 version) is not handling
> alpha-L-fucose links correctly - even when I use a correct alpha-linked
> model (from the server), and define the link and the sugar appropriately
> (see below), it comes back from the refinement with a beta-linkage.
>>
>> LINK         C1  NAG A 501                 ND2 ASN A 105
>> NAG-ASN
>> LINK         O6  NAG A 501                 C1  FUC A 506
>> ALPHA1-6
>> MODRES      NAG A  501  NAG-b-D
>> RENAME
>> MODRES      FUC A  506  FUC-a-L
>> RENAME
>>
>> Maybe someone of the hardcore REFMAC refinement guys (who is familiar
> with the libraries) would be willing to check if there is an issue with
> the dictionary for alpha-L-fucose or if I am still missing
> something?????
>>
>> Thanks for your help, cheers, Petra
>>
>>
>>
>>
>>> you can use
>>> http://www.glycosciences.de/modeling/sweet2/doc/index.php
>>>     to get a pdb file of your sugar
>>>
>>> and after fitting in density and refinement use
>>> http://www.dkfz-heidelberg.de/spec/glycosciences.de/tools/pdbcare/
>>>     to check the stereochemistry
>>>
>>> this should identify if there is a refmac dictionary problem
>>>
>>> your sugar is a "Core Fucosylated And Bisected N-glycan (N-Link 2)"
>>>     [see the sweet doc pages]
>>>
>>> you can make the IUPAC notation in plain ASCII
>>>
>>>   a-D-Manp-(1-6)+
>>>                 |
>>>                 |             a-L-Fucp-(1-6)+
>>>                 |                           |
>>>                 |                      b-D-GlcpNAc-(1-4)-Asn
>>>                 |                           |
>>>             b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+
>>>                 |
>>>                 |
>>>                 |
>>>                 |
>>>                 |
>>>   a-D-Manp-(1-3)+
>>>
>>> and drop this into sweet and get an idealised torsion angle(d) pdb
>>>
>>>
>>>         an o/p is www.ebi.ac.uk/~henrick/sug.pdb
>>>
>>> unfortunately the original pdb output is not exactly pdb
>>> you have to move the residue name column and the
>>> ASN is labelled as UNK
>>>
>>> the torsion angles are from the database
>>> http://www.glycosciences.de/modeling/glycomapsdb/
>>>
>>> if you want to check your fitted conformation with what is expected (a
> lot more freedom than a ramachandran but basically
>>>   the same type of plots)
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Kim HENRICK    [log in to unmask] ::telephone:  +44 (0) 1223 494629
>>>
>>
>>
>>
>
> *****************************************************
> Kelvin Luther
> Program in Molecular and Cellular Biology
> Stony Brook University
> Stony Brook, New York
> 11794  USA
> mailto:[log in to unmask]
> *****************************************************
>
>
>
> --
> Petra Verdino, PhD
> Research Associate
> The Scripps Research Institute, BCC206
> 10550 North Torrey Pines Road
> CA 92037 La Jolla, USA
> tel:1-858-784-2294
> fax:1-858-784-2980
>