[Demelerlab] AUC Collaboration: Sizing Amyloid Beta derived Oligomers

[Borries Demeler]

Hi Jason,
thanks for the PDB files, as I suspected we need new definitions for the
various non-canonical AAs. I get errors when running SOMO on the undefined
residues. I asked Emre from our group to suggest a way how to deal with
this. Presumably someone needs to edit the definitions for the unknown
residues. I'll give you some updates when I have them.

Regards, -borries

On Thu, Jul 6, 2023 at 11:37 PM Jason Zhu <jasonz13 at uci.edu> wrote:

> Dear Borries and the Demeler lab,
>
> As a follow-up to our conversation today, I've attached my slides, PyMOL
> models for the crystallographic F19Cha hexamer and the proposed NMR
> dodecamer based on a structural analog (PDB ID: 5v63). I broke up the
> subunits of the crystallographic hexamer and proposed NMR dodecamer into
> separate pdb files to make them easier to work with.
>
> In the meantime, I'll try adding Tris to my peptide, running samples on
> the nanodrop, purifying more F19Cha and will keep you posted.
>
> Thanks again for setting up this meeting and having so many members of
> your lab attend. Please feel free to reach out if there's anything you need
> from our end. I look forward to working with you all! :)
>
> Kind regards,
> Jason
>
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