I want to mutate an ALA to a CYS using COOT software, but I couldn't achieve my desired coordinates by clicking 'simple mutation' button. I found another button in COOT 'mutate and auto fit', but it asks for a map. Does anyone have an idea on what the map is and how I can generate one?
Thanks in advance.
First, Coot is a software intended to crystallographic model building and correction. So, when Coot asks for a map for fitting a residue's position, it is an electron density map in .mtz format that is required.
If you just want to mutate a particular residue, click on the "go to atom" or F6, then chose your residue. Coot will automatically center its view on the selected residue. Then, click on the "simple mutate" button, click on the residue you want to mutate, and choose by which residue you want to mutate it.
A problem can come from this, which is that there is a supplementary sulfur on the new side chain compared to Ala, and coot won't be able to optimize the position of this new atom. You can try then the "regularize zone" button on this particular residue (this option doesn't require a map), but you can't be sure that the obtained position for this new atom is realistic or not... If you want to move only this atom by yourself and choose its position, you can also do it with the "Edit Chi Angles" tool, which will allow you to rotate around the Ca-Cb bond and thereby move the sulfur without moving anything else...
Hop this helps, good luck
I agree with the above. If you want to use the map, as its always good to look at the electron density when mutating or analysing a structure, you can get it from the rcsb website. For mtz files pdbredo is a useful site, give the pdb number and it will give you an optimised structure if applicable and the refined mtz file.
Dear Yann-Vaï,
Thanks you so much. This is new to me and I really appreciate your sharing. Ill try it first and will get back to report.
Dear Stephen,
Thanks! The info you gave is really useful.