mutation using PyMOL

Question

[sina.pilot90]

Hi!

I need to perform an operation to mutate five amino acid residues in five positions of a pdb file to other 19 standard amino acid residues but I need a help with scripts (or commands).

Could anyone give a hint on how to do it ?

Thanks !

Answer 1

[João Rodrigues]

You would be better off using something like MODELLER, where you can then do a small restrained minimization of your mutated protein. In PyMOL, have a look at this thread of their mailing list.

Answer 2

[bieniekmat]

It is possible to do this in PyMOL.

Depending on what you want to do, you can either use the Wizard which allows you to mutate amino acids, or you can use the builder to cut bonds and insert new amino acids.

After stitching everything together, I used sculpting to relax the structure a bit. However, there did not seem to be any way to remove clashes ("clean" button does not work) - instead, I used gromacs to minimise the structure.