[PyMOL] separating multiple conformers

[<th...@br...>]

Hi,

I am modeling both an ADP and an AMP molecules in the same binding =20
site for my enzyme; occupancy at 50%.  I am trying to represent both =20
molecules as sticks however pymol connects the atoms that ADP atoms to =20
the AMP atoms in addition to the correct intramolecular bonds.  Is =20
there a way to prevent this from happening?

I have tried renumbering the two molecules but that doesn't seem to =20
work either.

Thanks in advance for any assistance.
Vu

Here is the pdb for the ligand:

ATOM   3317  O2A ADP C 300     -12.891 -31.977   0.219  0.50 13.89          =
 O
ATOM   3318  PA  ADP C 300     -11.985 -31.320  -0.791  0.50 11.99          =
 P
ATOM   3319  O1A ADP C 300     -11.373 -29.973  -0.515  0.50 13.45          =
 O
ATOM   3320  O3A ADP C 300     -12.595 -31.241  -2.295  0.50 15.19          =
 O
ATOM   3321  PB  ADP C 300     -14.063 -31.588  -2.912  0.50 15.05          =
 P
ATOM   3322  O3B ADP C 300     -14.089 -33.099  -2.944  0.50 17.83          =
 O
ATOM   3323  O2B ADP C 300     -15.064 -31.025  -1.914  0.50 18.59          =
 O
ATOM   3324  O1B ADP C 300     -14.162 -30.895  -4.245  0.50 19.02          =
 O
ATOM   3325  O5* ADP C 300     -10.845 -32.409  -1.042  0.50  9.81          =
 O
ATOM   3326  C5* ADP C 300      -9.842 -32.119  -2.001  0.50 10.91          =
 C
ATOM   3327  C4* ADP C 300      -8.684 -33.087  -1.844  0.50  9.33          =
 C
ATOM   3328  C3* ADP C 300      -9.032 -34.573  -1.896  0.50  9.63          =
 C
ATOM   3329  O3* ADP C 300      -9.242 -35.052  -3.249  0.50  8.90          =
 O
ATOM   3330  C2* ADP C 300      -7.855 -35.160  -1.134  0.50  8.90          =
 C
ATOM   3331  O2* ADP C 300      -6.678 -35.178  -1.953  0.50  9.51          =
 O
ATOM   3332  C1* ADP C 300      -7.612 -34.116  -0.038  0.50  8.69          =
 C
ATOM   3333  O4* ADP C 300      -8.058 -32.876  -0.567  0.50 10.93          =
 O
ATOM   3334  N9  ADP C 300      -8.485 -34.447   1.112  0.50  8.22          =
 N
ATOM   3335  C4  ADP C 300      -8.437 -35.592   1.790  0.50  8.39          =
 C
ATOM   3336  C5  ADP C 300      -9.471 -35.475   2.807  0.50  8.12          =
 C
ATOM   3337  N7  ADP C 300     -10.034 -34.267   2.665  0.50  7.40          =
 N
ATOM   3338  C8  ADP C 300      -9.438 -33.647   1.622  0.50  8.88          =
 C
ATOM   3339  N3  ADP C 300      -7.686 -36.716   1.682  0.50  7.55          =
 N
ATOM   3340  C2  ADP C 300      -7.900 -37.723   2.547  0.50  7.99          =
 C
ATOM   3341  N1  ADP C 300      -8.847 -37.696   3.503  0.50  7.64          =
 N
ATOM   3342  C6  ADP C 300      -9.652 -36.630   3.682  0.50  8.15          =
 C
ATOM   3343  N6  ADP C 300     -10.592 -36.602   4.662  0.50  6.97          =
 N
ATOM   3344  O3P AMP C 300     -12.386 -32.366  -2.017  0.50 15.02          =
 O
ATOM   3345  P   AMP C 300     -11.925 -31.677  -0.753  0.50 10.92          =
 P
ATOM   3346  O1P AMP C 300     -11.847 -30.186  -0.880  0.50 11.64          =
 O
ATOM   3347  O2P AMP C 300     -12.551 -32.108   0.554  0.50  9.93          =
 O
ATOM   3348  O5* AMP C 300     -10.360 -32.000  -0.546  0.50 11.26          =
 O
ATOM   3349  C5* AMP C 300      -9.423 -31.767  -1.590  0.50 10.64          =
 C
ATOM   3350  C4* AMP C 300      -8.421 -32.915  -1.587  0.50 11.52          =
 C
ATOM   3351  C3* AMP C 300      -9.037 -34.271  -1.900  0.50 11.54          =
 C
ATOM   3352  O3* AMP C 300      -9.264 -34.467  -3.299  0.50 13.20          =
 O
ATOM   3353  C2* AMP C 300      -8.024 -35.226  -1.313  0.50 10.05          =
 C
ATOM   3354  O2* AMP C 300      -6.891 -35.236  -2.197  0.50 11.30          =
 O
ATOM   3355  C1* AMP C 300      -7.642 -34.492  -0.031  0.50 10.00          =
 C
ATOM   3356  O4* AMP C 300      -7.815 -33.102  -0.294  0.50  9.81          =
 O
ATOM   3357  N9  AMP C 300      -8.539 -34.824   1.112  0.50  8.85          =
 N
ATOM   3358  C4  AMP C 300      -8.487 -35.983   1.773  0.50  8.44          =
 C
ATOM   3359  C5  AMP C 300      -9.484 -35.904   2.839  0.50  7.99          =
 C
ATOM   3360  N7  AMP C 300     -10.054 -34.689   2.756  0.50  8.54          =
 N
ATOM   3361  C8  AMP C 300      -9.465 -34.047   1.707  0.50 10.10          =
 C
ATOM   3362  N3  AMP C 300      -7.745 -37.107   1.621  0.50  9.33          =
 N
ATOM   3363  C2  AMP C 300      -7.922 -38.163   2.444  0.50 10.24          =
 C
ATOM   3364  N1  AMP C 300      -8.841 -38.161   3.428  0.50  9.63          =
 N
ATOM   3365  C6  AMP C 300      -9.634 -37.099   3.677  0.50  9.56          =
 C
ATOM   3366  N6  AMP C 300     -10.544 -37.126   4.684  0.50  8.49          =
 C