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/*
<http://www.beakycoot.com/pudding.html>******** 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_///
<file://www.beakycoot.com/pudding.html>///// -/ _Similar_
<file:///search?hl=en&q=related:www.beakycoot.com/pudding.html+adding+sugars+in+coot&sa=X&ei=r6YhS-T1F4PQlAeP2ZT8CQ&ved=0CAgQHzAA>//
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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