Editing Mutagenesis

= Mutagenesis =
PyMol has a '''Mutagenesis Wizard''' to make mutagenesis very easy for the end user.

In [[rotkit]], a function has been made to call a mutagenesis.

As of PyMOL version [https://pymol.org/dokuwiki/?id=media:new22 2.2], users may now perform base mutations in nucleotide chains.
== Walk-through ==
To mutate a residue follow these easy steps:
<OL>
<LI>Load a PDB file<BR><BR>

[[Image:Mutag1.png|180px|none]]
<LI>Under the '''Wizard''' menu select '''Mutagenesis'''<BR><BR>

[[Image:Mutag2.png|180px|none]]
<LI>In the PyMol viewer window select a residue<BR><BR>

[[Image:Mutag3.png|180px|none]]
<LI>Select '''No Mutation''' and select resultant residue<BR><BR>

[[Image:Mutag4.png|180px|none]]
<LI>Selecting the rotamer you think better fits your structure. <BR><BR>

    Several side chain orientations (rotamers) are possible. You can use
    the back-and-forth movie controls (lower right corner) to display (in white) each of the rotamers available for
    this residue in PyMOL, whose current and total numbers are shown in the (green) Frame info. The rotamers
    are ordered according to their frequencies of occurrence in proteins, shown as a red percentage at the mutation
    object, which exists while mutagenesis is being performed.  <BR><BR>



<LI>Select Apply
<LI>Select Done
</OL>

== Explanation of colour codes ==

From [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06196.html]:

The visible disks & colors in the Mutagenesis Wizard indicate pairwise overlap of atomic van der Waals radii.  The intent is to provide a qualitative feedback regarding contacts and bumps.

Short green lines or small green disks are shown when atoms are almost in contact or slightly overlapping.  Large red disks indicate signficant van der Waals overlap.  Everything else lies between those extremes.



[[Category:Tutorials|Mutagenesis]]
[[Category:Wizards]]