Hi everyone, I am using the pyTMs plug in on Pymol to phosphorylate a particular threonine in my protein. I am having difficulty in selecting only one or two residues - it seems I can only phosphorylate all serines/theronines. Does anyone know how to fix this?
Try the SwissSideChain Plug-in https://www.swisssidechain.ch/visualization/pymol.php available for PyMOL https://pymol.org/2/ and Chimera https://www.swisssidechain.ch/visualization/chimera.php
You can try Maestro software to edit (Phosphorylate) particular residue with energy minimization. Energy minimization is required step while converting (mutate) or editing (like Phosphorylation), so Maestro is a very suitable software for it.
Maestro is also Schrodinger's software like Pymol. You can use free for academic.
If you are using the PyTMs plugin, you can select the residues you want to phosphorylate in the sequence before opening the plugin. Then under "Selection" you can change the word "all" to "sele". It should only phosphorylate the residues you select.
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