Hej Raag,
my name is Andreas and I wrote PyTMs back for my PhD. It essentially uses
PyMOLs basic editing functions to build PTMs onto protein models.
PyTMs is a simple tool and has its clear restrictions, but generally it is
nice to play around with and explore hypotheses with.
The challenge is that drawing conclusions about the impact of PTM on
tertiary structure is very limited and that there will be increasing
uncertainty about positioning of atoms the larger the PTM is. Also charge
effects are an issue and overall one will increasingly be confronted
with questions regarding Molecular Dynamics.
As far as your project is concerned you can rather easily add a Tyrosine
(or custom fragments) using the builder in PyMOL:
https://pymolwiki.org/index.php/Modeling_and_Editing_Structures
In editing mode, you can select an atom to extend on and manually select:
*build-->residue *from the menu
Additionally I'd also point out the API command to experiment with:
editor.attach_amino_acid("pk1","tyr")
If you have any questions about the editing or PyTMs feel free to PM me.
Unfortunately, I can't promise to update the plugin unless I find the spare
time to invest.
Cheers,
Andreas
On Wed, Apr 12, 2017 at 9:36 AM, Raag Saluja <saluja.r...@gmail.com> wrote:
> Hi!
>
> PyTMs is wonderful and permits me to really play around with a lot of
> different PTMs!
>
> In PyTMs, I can find some of the PTMs that I need to work on (acetylation
> and phosphorylation) for my PhD. However, there are some PTMs that I need
> to work on for my PhD, but I can't find those features in PyTMs. I need to
> study (1) tyrosination/detyrosination, polyglutamylation and
> polyglycylation and (2) PTMs on the C-termini. How do I go about those?
>
> This might sound like I'm asking too much, but can you please include
> these in PyTMs as well? PyTMs is really user friendly. It would be
> wonderful if you can please do that!
>
> Regards,
> Raag
>
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