Re: [PyMOL] separating multiple conformers

> unbond selection1, selection2

On Wednesday 29 August 2007 18:16, th...@br... wrote:
> 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
>
>
>
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-- 








______________________________________
Stuart T. Endo-Streeter
Structural Biology and Biophysics
Dept. Biochemistry
LSRC C266
Duke University
919-681-1668
stu...@du...