To add to this,
It depends on what you mean by "handles" - certainly the gui and the inter-residue consensus distance
restraints will be missing, but you can get some way to where you need to go with a few scripting bits and bob.
First download and install (for some value of $coot_prefix) the appropriate reference internal coordinates
table, find it here:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/link-by-torsion-to-NAG-core-NAG-SER.tab
$ cp link-by-torsion-to-NAG-core-NAG-SER.tab $coot_prefix/share/coot
Then in Coot, Scripting, Python:
add_synthetic_pyranose_planes()
use_unimodal_pyranose_ring_torsions()
# I used as an example the beautiful 4gyw, adding a NAG to B21 SER:
add_linked_residue(0, 'B', 21, '', 'NAG', 'NAG-SER', 0)
# there is a problem with SER OG, but it will be good enough for refmac.
# screeny attached.
# you can then add to the new NAG buy using an analog of the above
# add_linked_residue command or use the Glyco -> N-linked Glycan Addition
# dialog in "Expert" mode
Paul.
On 23/07/2018 18:29, Garib Murshudov wrote:
> There are
> NAG-SER, NAG-THR
> links in the monomer library. I do not know if you are looking for these links.
>
> If you need any other link you can use AceDRG to generate them.
>
> Regards
> Garib
>
>
>
>> On 23 Jul 2018, at 23:07, Goran Bajic <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>> Hi all,
>>
>> I may have an O-linked glycan in one of my structures and I was wondering if someone has any experience
>> building these? I think COOT only handles N-linked glycans.
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atom C1 C based-on 1 OG 1 CB 1 CA bond-length: 1.44617 angle: 124.10401 tors: 152.69329
atom C2 C based-on 0 C1 1 OG 1 CB bond-length: 1.52397 angle: 114.86803 tors: 52.46979
atom C3 C based-on 0 C2 0 C1 1 OG bond-length: 1.52505 angle: 110.61181 tors: 154.78196
atom C4 C based-on 0 C3 0 C2 0 C1 bond-length: 1.52092 angle: 109.54626 tors: -53.81838
atom C5 C based-on 0 C4 0 C3 0 C2 bond-length: 1.52123 angle: 108.85258 tors: 56.33237
atom O5 O based-on 0 C5 0 C4 0 C3 bond-length: 1.40825 angle: 109.05598 tors: -59.16742
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