Open whatif and give the following commands. (Substitute your PDB file for 1crn.pdb and the number of the residue you want to mutate for 13 used in this example.)
getmol
1crn.pdb Or your pdb file
crn Just a name for withing whatif
colour Go to the color menu list
colzns Color one residue (by zone) so you can see it
13 Or your residue number
0 To exit the loop of range input
red Some colors work others don't
graphic Go to the graphics menu list
shoall Display what we have done in object 1a
1
a
go Go to the graphics screen and look at your molecule
[click]CHAT Click the green box to return to command screen
mutate Mutate residue 13 to an ARG
13
n
arg
%colzns The percent is because we are not in the color menu
13 just now. We will color the new arg red also
0
red
shoall Display what we have done in a second object 2a
2 (This will be MOL2 on the graphics screen)
b
go Go to the graphics screen and click MOL1 on/off
[click]CHAT Return to the command screen
debump Find a rotomer that has the fewest bumps
13
0.25 Default
3 Default
%colzns Color the debumped residue also
13
0
red
shoall Display what we have done in a third object on the
3 graphics screen
c (This will be MOL3 on the graphics screen)
go Go to the graphics screen and click off MOL1
and click on/off MOL2
[click]CHAT Click the green box to return to command screen
soup Go to the soup menu list
makmol Make a new PDB file
[return]
filname.pdb The name of your mutated structure PDB file
all Include all residues
0 To exit the loop of range input
fullstp To quit the program
y