There is no excuse for using MAN to mean both alpha and beta mannose.  
It is easy to take a MAN-b-D.cif file and modify it to a BMA.cif.  BMA 
is already in the monomer library that comes with ccp4 (but I think it 
does not have geometry descriptions), and the last time I checked, there 
was not a BMA.cif in the default library that ships with phenix.refine, 
which makes using the standard beta-D-mannose monomer name one tiny step 
more difficult then using MAN for both alpha and beta mannose. No 
surprise then that nearly 30% of all sugar entries have incorrect names 
and geometries in the PDB (according to the paper that describes PDB-care).

Engin

On 12/22/09 9:29 AM, Damian Ekiert wrote:
> For an "ideal" glycan, you could used a model from a high resolution 
> structure, or something that has been energy minimized, etc.  Mostly I 
> find this helps in getting the sugars in about the right place 
> (keeping bond lengths and angles reasonable).
>
> I perhaps could stand to fiddle more and maybe I'll look through the 
> updated documentation.  Last I tried, the Asn-NAG1 linkage wasn't 
> enforced, with would allow the whole glycan to slide down into the 
> protein, or off into space.  I am typically building relatively small 
> glycans (2-5 residues) into ~3A data, so the density itself doesn't 
> keep things in place very well.
>
> Regarding BMA vs MAN: When I have tried to used BMA in REFMAC, it 
> doesn't seem to recognize it and requires a library file.  But if you 
> use MAN, it adds a MODRES record to the header, enforcing beta-mannose 
> geometry.  Not sure if this is just a REFMAC version issue or what.
>
> Best,
>
> Damian
>
>
>
>
> Paul Emsley wrote:
>> If I can chip into this somewhat sacrilegiously-named thread
>>
>> 1) I *would* use real-space refinement :), specifically Sphere 
>> Refinement.  You can dial down the
>>     density weight if needed, of course.
>>
>> 2) the documentation on refining carbohydrates in Coot has recently 
>> been updated
>>
>> http://www.biop.ox.ac.uk/coot/doc/coot/Refining-Carbohydrates.html
>>
>> 3) Coot does not (yet) correct chiral centre inversions in glycosidic 
>> linkages on refinement
>>
>> 4) or delete the O1s :)
>>
>> Paul.
>>
>>
>>
>> Robbie Joosten wrote:
>>> Dear Steve,
>>>
>>> I would also use Damian's approach, but the sequence of the core 
>>> should be
>>> NAG-NAG-BMA-(MAN)2. This is improtant because the correct 
>>> stereochemistry
>>> restraints for beta-mannose can only be applied when you call the 
>>> residue
>>> BMA.
>>> Building carbohydrates also comes with special validation requirements.
>>> PDB-care and CARP are both very usefull. Unfortunately, the service is
>>> currently down (http://www.dkfz.de/spec/glycosciences.de). Just make 
>>> sure
>>> the links between your carbs are correct and, please, remove the O1 
>>> atoms
>>> when needed ;)
>>>
>>> Cheers,
>>> Robbie Joosten
>>>
>>> ----------------------------------------
>>>> Date: Mon, 21 Dec 2009 17:48:31 -0800
>>>> From: [log in to unmask]
>>>> Subject: Re: [ccp4bb] Coot pudding? (a.k.a N-linked carbohydrate 
>>>> addition)
>>>> To: [log in to unmask]
>>>>
>>>> Steve,
>>>>
>>>> My general strategy is to start with an "ideal" glycan (an Asn 
>>>> linked to
>>>> NAG-NAG-(MAN)3 ) and superimpose the Asn on the residue from my 
>>>> protein.
>>>> Then you can move the whole glycan as a rigid body until the Asn and
>>>> first NAG are roughly positioned. Then you can tweak any sugars 
>>>> further
>>>> out on the chain to get them to fit. Unless you have really great
>>>> density, usually it is best to avoid real pace refine zone. Better to
>>>> fit the sugars using the manual rigid body fitting tools, do the best
>>>> you can, then REFMAC usually brings them in OK.
>>>>
>>>> I have some models that I could send you if you need them.
>>>>
>>>> Best,
>>>>
>>>> Damian Ekiert
>>>>
>>>>
>>>>
>>>> Soisson, Stephen M wrote:
>>>>> Hi everyone-
>>>>>
>>>>> I was searching for some information on what might be the best way to
>>>>> add N-linked sugars in coot, and Google has let me down. Searching
>>>>> "adding sugars in coot" returns a very nice recipe for Coot Pudding.
>>>>>
>>>>> ***_Recipe for_/ Coot//__/_ Pudding - American_/ Coots/*
>>>>> ******** It has plenty of fat,/
>>>>> sugar/, and starch, and probably some calcium from the milk.* ...* 
>>>>> The/
>>>>> coots/ will not tolerate/ adding/ eggs in any form, so this is an 
>>>>> egg*
>>> ...*
>>>>> ///_www.beaky_//_*coot*.com/pudding.html_///
>>>>> ///// -/ _Similar_
>>>>> //
>>>>>
>>>>>
>>>>>
>>>>> I did not know that coots had such an aversion to eggs. :)
>>>>>
>>>>> Anyway, would anyone have any top tips on adding N-linked sugars 
>>>>> using
>>>>> coot? I can import the NAG monomers, but linking them up to the 
>>>>> protein
>>>>> seems non-trivial
>>>>>
>>>>> Many thanks in advance,
>>>>>
>>>>> Steve
>>>>>
>>>>>
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-- 
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111