Re: [PyMOL] Nonsense mutagenesis

[Jared S. <jar...@co...>]

Hi Jevin -

Depending on how far the termination codon mutation is from the end, it may
work to just delete residues from 415 onward.  However, if this would
delete a substantial chunk of the protein, the real structure of the
truncated polypeptide may differ significantly from the crystal structure
of the full protein, so you should definitely proceed with caution when
interpreting any downstream results.

To apply this naive version of the Gln415Ter nonsense mutation, assuming
the model is called "mystructure", the mutation is on chain A, and the
highest residue number on the chain is 999, you can do something like:

    remove mystructure and chain A and resi 415-999

Hope that helps.

Cheers,
Jared



On Thu, Jun 23, 2022 at 11:24 AM Jevin Parmar <jev...@pe...>
wrote:

> Hi there,
>
>
>
> I’m trying to conduct some mutagenesis on a protein, but I have found that
> PyMol only currently does mutagenesis from one amino acid to another. Is
> there a way to conduct mutagenesis for point mutations resulting in a
> termination codon (eg. p.Gln415Ter)?
>
>
>
> Addtionally, I am unsure how to do nucleotide mutagenesis on a PDB file
> that only had an AA sequence. Is there a way to change the amino acid
> sequence to a nucleotide sequence?
>
>
>
> Thank you in advance!
>
>
>
> Jevin Parmar
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