Mutating a residue


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