Hi,
I am modeling both an ADP and an AMP molecules in the same binding
site for my enzyme; occupancy at 50%. I am trying to represent both
molecules as sticks however pymol connects the atoms that ADP atoms to
the AMP atoms in addition to the correct intramolecular bonds. Is
there a way to prevent this from happening?
I have tried renumbering the two molecules but that doesn't seem to
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
