Jonas Vasur wrote:
> Hi Paul,
>
> Thank you for your continued hard work with Coot (I just downloaded
> 0.3.3). I am working with oligosaccharide ligands. I build them into
> the ligand's electron density using coot. I need help on the
> following:
>
> 1) How can I get coot to recognize a covalent bond within an
> oligosaccharide? Is proximity the only determining aspect here
Yes. Coot determines the type of glycosidic bond.
There is the standard issue of tandem residue numbers, of course.
> (and
> then hope that it turns out right in refmac)?
That I don't know about.
> 2) Is it advisable to build oligosaccharides monosaccharide by
> monosaccharide into the electron density in coot?
I'd say so. Except sucrose seems to be a "monomer" in the Refmac library.
> 3) Chirality check does not seem to work for sugars.
You mean the validation tool rather than the refinement?
If so please send an example.
> D-glucose can
> automagically transform itself into an L-glucose when Real Space
> Refine Zone is applied
> and a 4C1 chair conformation can become a 1C4
> chair conformation.
Yes, chiral centres can be inverted under real space refinement
currently. Decreasing the weight makes this happen less frequently.
> The D-glucose cif file is from the coot library
Refmac library :)
> (with chirality specified for the carbons). Are there any plans on
> changing this
Yes, definitely.
> or have I missed some important function or option?
No.
Currently, there is only suffering. It's things like this that stop
coot being at (or approaching) version 1.0 :-/
Paul.
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