On 09/03/2018 17:29, Erik Klontz wrote:
>
>
> I have solved a few Fc crystal structures, and am having trouble building the full length glycans onto them.
> I've been using the coot "glyco" module which I really like,
Glad to hear it.
> but I don't see any options for adding B(1-2)
> NAG. I'm using the latest version of coot on windows.
I guess that 0.8.9's Glyco module has not been ported to Python. Coot-0.8.9's Glyco module is an improvement
over previous version. I am planning a (small?) modification for 0.8.9.1.
> I've seen screenshots from other people's modules that
> show this (and many other linkages) as options. Is this only available on linux or is there something I need
> to do to access the full module?
To be clear, it's not a Linux vs everything problem, it's a guile vs non-guile problem.
Personally, I'd try to install a coot on the Ubuntu Linux subsystem that comes with Windows these days.
>
>
> Alternatively, is there an easier way of doing this? I've tried building the glycans using GLYCAM, but I
> can't figure out any way of linking them to the asparagine so the Asn-glycan bond parameters are reasonable.
If you put it in the "right place" (less than 2.2A between the C1 and ND2) and if the glycan is in the same
chain as your protein, then coot will make the linkage for you in refinement. You can also do a Extensions
-> Modelling -> Make Link, which adds a link record to the exported coordinates files, so that other
programs know that there is a link there.
Paul.
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