I'm trying the edit the orientation of some side chains in a homology protein model I made. Can I use PyMOL for such tasks? If so, could anyone navigate me to some online tutorials? If not, what other softwares would be suitable?
Thank you so much! Any help will be greatly appreciated!
Yes, but the Chimera can energy minimized the strucutre so it is good. I never used full version of PyMol so i am not aware of its full capabilites. If it can EM the structure, then edit the strucutre and energy minmized it.
In PyMol, you can use the "Mutagenesis Wizard" (menu "Wizard", item "Mutagenesis", "Protein") to mutate individual residues and cycle through the various side chain rotamers using the movie controls. You can choose whether to use the backbone dependent or backbone independent Dunbrack library of side chain conformation. Clashes are indicated by red disk, and the strain for each pose is listed in the feedback window. https://pymolwiki.org/index.php/Mutagenesis
https://www.youtube.com/watch?v=M-VCBz83nfs
https://www.youtube.com/watch?v=vQJCPgr5drk
https://www.youtube.com/watch?v=p-IEBIlu9m8
While this is quick way to check whether an individual side chain clash can be relieved by a rotamer change, for serious modelling I personally prefer to use Rosetta fixed backbone design (fixBB) to optimise the side chain packing. However, Rosetta has a fairly steep learning curve. For easier access, you can also use the Rosie server https://rosie.graylab.jhu.edu/fixbb/documentation
You mean changing the angles of your model or entire residues? Coot will do that too, which is kind of more complete than Pymol or any visualization softwares. If you need just a global energy minimization, you may choose different softwares that include Force Fields, or even Isolde
Energy minimization is the wrong strategy to correct side chain clashes, as it will not jump the energy barrier to a different side chain rotamer. Optimally, when building a protein model, you first resolve severe side chain clashes by rotamer changes before you do an energy minimization. PyMol is not the right tool to do any energy minimization. Energy minimization does not resolve any modelling errors, it simply spreads their effects over a larger part of the molecule, and therefore makes them harder to detect.
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