There is a way to do this in pymol. Change the mouse mode to editing mode and
click the two ends of the loop, then you should be able to drag it around. I
don’t remember exactly how, but hopefully this helps.
Alternatively, you could delete the loop and input the structure into modeller
and ask for several models and hopefully one of them would be open
Best wishes
James
On 2 Apr 2025, at 16:43, Rafael Marques <rafael_mmsi...@hotmail.com> wrote:
Hi everyone,
I am struggling to think about a fast way to move a loop away from a protein
domain. I have an alphafold model of a multidomain transmembrane protein that,
for a presentation, I would like to "adjust". Between the intracellular bit of
it and the extracellular part there is a intrinsically disordered loop. I would
like to "open" this loop to emphasize that the domains are distant from each
other. And I can not think about any other way of doing it if not changing
manually the phi and psi angles of every single amino acid in this loop, which
I do not want to do. Any suggestion?
Best wishes
______________________________________________________
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +44 07861 273773
"A sorte acompanha uma mente bem treinada"
________________________________________________
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