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CCP4BB  December 2009

CCP4BB December 2009

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Subject:

Re: Coot pudding? (a.k.a N-linked carbohydrate addition)

From:

Paul Emsley <[log in to unmask]>

Reply-To:

Paul Emsley <[log in to unmask]>

Date:

Tue, 22 Dec 2009 14:59:59 +0000

Content-Type:

text/plain

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text/plain (106 lines)

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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