Hi Leo,
you should not need an additional cif file for coot but you might need
to generate one for reciprocal space refinement. If you use REFMAC it
might 'fail' in the first attempt with the message 'new ligand
encountered' or something similar. It will, however, generate a single
cif file for the sugar if it recognizes the monosaccharides and the
glycosidic linkage you have created in coot, using the descriptions
from the REFMAC library. You can then look at this cif file and
provide it for future refinement runs in REFMAC. It is a good idea to
keep checking if the glycosidic bond is identified correctly and
restrained accordingly in every REFMAC run after you introduced the
ligand/glycosylation.
I find it a lot harder to achieve correct sugar refinement with
phenix, although elbow should techically be able to create a cif file
for sugars just like REFMAC. The prodrug server is a bad idea, as
pointed out, because the library restraints for sugars are not used if
the sugar rings are not identified with the correct three letter
abbrevations in your pdb file.
If you have a larger oligosaccharide and good density it might be
easiest to start by getting a similar sugar model from a deposited pdb
file. Place this molecule in your sugar density using rigid body
refinement, then start to manipulate single rings from the template so
that they fit your density best. Often this is a matter of rotating
the individual rings around their glycosidic bonds. When you try this
procedure be aware that there are lots of distorted sugar rings in the
pdb, so make sure you start from a good template.
Good luck,
Baerbel
Zitat von Lie Ma <[log in to unmask]>:
> Thank you, Paul.
>
> And do I need to provide additional cif file which describe the bond?
>
> Leo
>
> On Sep 4, 2014, at 2:23 PM, Paul Emsley <[log in to unmask]> wrote:
>
>> On 04/09/14 19:06, Lie Ma wrote:
>>> Hello all,
>>>
>>> I am trying to make a model of an oligosaccharide which contains
>>> several sugar monomers. I obtained the monomers from coot library
>>> and put them into the electron density. But I don't know how to
>>> make covalent bond between these monomers.
>>
>> If you are using Coot, you can use Extensions -> Modelling -> Make Link.
>>
>> If you sugar monomers are reasonably placed Coot's Sphere Refine
>> will determine the correct link types on the fly (it doesn't
>> believe what's in the PDB file).
>>
>>>
>>> I tried to use PRODRG to generate a model and it gave me one big
>>> ligand consisting of several monomers.
>>
>> Yes, that's not the way to do it...
>>
>>> However, what I want is to have a chain contains several
>>> monomers, and each monomers acts like a residue.
>>
>> Indeed.
>>
>>
>> Paul.
>>
>
--
Bärbel Blaum, Ph.D.
Interfakultäres Institut für Biochemie (IFIB)
Hoppe-Seyler-Strasse 4
D-72076 Tübingen
Germany
+49 70 71 29 73 375
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