Swiss-PdbViewer allows to browse a
rotamer library in order to change amino acids sidechains.
This can be very useful to quickly evaluate the putative
effect of a mutaion before actually doing the lab
To initiate a mutation, simply click on the mutation tool
located at the top of the display window. You will be
prompted to select a group, which is readily made by
clicking on any atom of the desired amino acid. Then a
pop-up menu will let you select the new amino acid type.
Note: clicking outside the list, as well as
hitting the "return" or "enter" key will automatically
select the rotamer library of the current amino acid.
At this point, the current sidechain will be replaced by
the "best" rotamer of the new amino acid, and the mutation
tool will appear in inverse video to signify that a mutation
is under process.
The "best" rotamer is the one that totalize the
lowest score according to the formula:
score = (4 x NbClash with backbone N CA and C atoms) +
(3 x NbClash with backbone O atoms) +
(2 x NbClash with sidechains atoms) -
NbHbonds - 4 x Nb SSbonds
The current rotamer number is displayed just below the
tools in the Display Window. You may obtain something like:
rotamer: 4/16 score: -1
which signifies that rotamer 4 out of 16 available has
been choosen. This display is updated each time you change
the rotamer by clicking on one of the little arrows that
come below the mutate tool, or by hitting the "*" key of the
numerical keyboard. Note that holding the "shift" key while
hitting the "*" key will select the previous rotamer instead
of the next one.
Putative H-bonds will appear in green, and steric
hindrances in purple. Note that they will be drawn only if
the group that makes the contact is visible, so think to
enlarge the view around the group to mutate before
proceeding (or even after see below)
You can freely rotate, move and resize the molecule, as well
as measure distances, display, undisplay, groups and so
Once you're done with your experimentations, you can end the
"mutation" process by clicking once again on the mutation
tool. You will be prompted for accepting or discarding the
mutation (which will put back the initial group sidechain).