SNPs can also be created by removing the GUI Chimera offers and manually changing residues. For instance, if you wanted to change isoleucine (ILE) to leucine (LEU), then you would find the ILE in the PDB and remove everything that was not the atoms named C, CA, N, or O.
Your original ILE
ATOM 129 N ILE 10 -15.372 24.194 -43.088 1.00 0.00
ATOM 130 H ILE 10 -16.116 24.609 -42.545 1.00 0.00
ATOM 131 CA ILE 10 -14.509 23.251 -42.446 1.00 0.00
ATOM 132 HA ILE 10 -13.546 23.173 -42.950 1.00 0.00
ATOM 133 CB ILE 10 -14.289 23.510 -40.982 1.00 0.00
ATOM 134 HB ILE 10 -13.900 24.518 -40.840 1.00 0.00
ATOM 135 CG2 ILE 10 -15.631 23.370 -40.244 1.00 0.00
ATOM 136 HG21 ILE 10 -16.020 22.362 -40.385 1.00 0.00
ATOM 137 HG22 ILE 10 -15.482 23.556 -39.180 1.00 0.00
ATOM 138 HG23 ILE 10 -16.343 24.093 -40.643 1.00 0.00
ATOM 139 CG1 ILE 10 -13.167 22.603 -40.448 1.00 0.00
ATOM 140 HG12 ILE 10 -13.563 21.588 -40.404 1.00 0.00
ATOM 141 HG13 ILE 10 -12.348 22.642 -41.167 1.00 0.00
ATOM 142 CD1 ILE 10 -12.652 23.009 -39.067 1.00 0.00
ATOM 143 HD11 ILE 10 -13.470 22.970 -38.348 1.00 0.00
ATOM 144 HD12 ILE 10 -11.863 22.324 -38.757 1.00 0.00
ATOM 145 HD13 ILE 10 -12.255 24.023 -39.110 1.00 0.00
ATOM 146 C ILE 10 -15.173 21.926 -42.614 1.00 0.00
ATOM 147 O ILE 10 -16.368 21.785 -42.360 1.00 0.00
becomes
ATOM 129 N ILE 10 -15.372 24.194 -43.088 1.00 0.00
ATOM 131 CA ILE 10 -14.509 23.251 -42.446 1.00 0.00
ATOM 146 C ILE 10 -15.173 21.926 -42.614 1.00 0.00
ATOM 147 O ILE 10 -16.368 21.785 -42.360 1.00 0.00
Finally, to change the SNP residue, change the residue name (resname) from ILE to LEU.
ATOM 129 N LEU 10 -15.372 24.194 -43.088 1.00 0.00
ATOM 131 CA LEU 10 -14.509 23.251 -42.446 1.00 0.00
ATOM 146 C LEU 10 -15.173 21.926 -42.614 1.00 0.00
ATOM 147 O LEU 10 -16.368 21.785 -42.360 1.00 0.00
Now you have what LEaP will see as a leucine, auto-filling the missing atoms. You can just leave the wonky non-sequential numbering, as LEaP also renumbers everything when it runs.