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
>>>>
>>>>
>>>> Notice: This e-mail message, together with any attachments, contains
>>>>
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