Dear Bob,
While preparing a morph from 5cl3 to 5cle, I re-ordered the hetero atoms
in 5cle so as to be in the same order as the homologous atoms in 5cl3.
This separated [3DR]6:B.P from the other 3DR atoms. The result is that
this phosphorus, while it remains hetero, is deemed by Jmol to be
neither ligand nor solvent nor DNA. I can live with this, but I am
reporting it in case it is a bug.
Tested with Jmol application dated November 18, 2015.
Example files:
http://bioinformatics.org/molvis/tmp/5cle-ligand.pdb
http://bioinformatics.org/molvis/tmp/reordered-ligand.pdb
Contents of example files:
ORIGINAL order from 5cle ([3DR]6:B.P is ligand)
HETATM 1 O5' 3DR B 6 40.400 -4.134 11.144 1.00
16.98 O
*HETATM 2 P 3DR B 6 40.429 -5.572 10.443 1.00
17.42 P *
HETATM 3 OP1 3DR B 6 41.434 -5.662 9.357 1.00
18.41 O
HETATM 4 OP2 3DR B 6 40.671 -6.600 11.482 1.00
19.96 O
HETATM 5 C2' 3DR B 6 40.069 -0.707 13.038 1.00
25.11 C
HETATM 6 C5' 3DR B 6 40.150 -3.117 10.183 1.00
20.01 C
HETATM 7 C4' 3DR B 6 39.863 -1.817 10.934 1.00
17.65 C
HETATM 8 O4' 3DR B 6 38.569 -1.913 11.598 1.00
19.68 O
HETATM 9 C1' 3DR B 6 38.611 -1.154 12.821 1.00
20.01 C
HETATM 10 C3' 3DR B 6 40.891 -1.550 12.055 1.00
23.32 C
HETATM 11 O3' 3DR B 6 41.949 -0.747 11.542 1.00
25.20 O
HETATM 12 N9 ADK B 101 38.704 -4.026 15.100 1.00
24.10 N
HETATM 13 C4 ADK B 101 38.277 -4.217 16.354 1.00
19.29 C
HETATM 14 N3 ADK B 101 37.775 -3.385 17.350 1.00
35.42 N
HETATM 15 C2 ADK B 101 37.434 -3.931 18.532 1.00
28.39 C
HETATM 16 N1 ADK B 101 37.558 -5.221 18.755 1.00
24.56 N
HETATM 17 C6 ADK B 101 38.031 -6.073 17.825 1.00
29.43 C
HETATM 18 N6 ADK B 101 38.164 -7.496 18.102 1.00
23.29 N
HETATM 19 C5 ADK B 101 38.405 -5.601 16.602 1.00
19.32 C
HETATM 20 N7 ADK B 101 38.896 -6.144 15.497 1.00
17.81 N
HETATM 21 C8 ADK B 101 39.069 -5.183 14.606 1.00
19.82 C
HETATM 22 C3A ADK B 101 37.649 -2.030 17.097 1.00
31.68 C
REORDERED (coordinates differ because this was aligned with 5cl3;
[3DR]6:B.P is NOT ligand):
*HETATM 2424 P 3DR B 6 59.344 -7.302 54.550 1.00
17.42 P*
HETATM 2438 N1 ADK B 101 56.456 -6.944 62.856 1.00
24.56 N
HETATM 2437 C2 ADK B 101 56.354 -5.651 62.639 1.00
28.39 C
HETATM 2436 N3 ADK B 101 56.707 -5.105 61.460 1.00
35.42 N
HETATM 2435 C4 ADK B 101 57.198 -5.940 60.462 1.00
19.29 C
HETATM 2441 C5 ADK B 101 57.302 -7.327 60.703 1.00
19.32 C
HETATM 2439 C6 ADK B 101 56.917 -7.799 61.923 1.00
29.43 C
HETATM 2440 N6 ADK B 101 57.026 -9.225 62.193 1.00
23.29 N
HETATM 2442 N7 ADK B 101 57.788 -7.873 59.597 1.00
17.81 N
HETATM 2443 C8 ADK B 101 57.979 -6.911 58.711 1.00
19.82 C
HETATM 2434 N9 ADK B 101 57.632 -5.750 59.210 1.00
24.10 N
HETATM 2431 C1' 3DR B 6 57.593 -2.866 56.945 1.00
20.01 C
HETATM 2426 OP2 3DR B 6 59.566 -8.339 55.585 1.00
19.96 O
HETATM 2427 C2' 3DR B 6 59.058 -2.445 57.168 1.00
25.11 C
HETATM 2425 OP1 3DR B 6 60.351 -7.404 53.467 1.00
18.41 O
HETATM 2432 C3' 3DR B 6 59.869 -3.296 56.183 1.00
23.32 C
HETATM 2433 O3' 3DR B 6 60.941 -2.509 55.677 1.00
25.20 O
HETATM 2444 C3A ADK B 101 56.605 -3.747 61.214 1.00
31.68 C
HETATM 2429 C4' 3DR B 6 58.840 -3.541 55.058 1.00
17.65 C
HETATM 2430 O4' 3DR B 6 57.542 -3.618 55.718 1.00
19.68 O
HETATM 2428 C5' 3DR B 6 59.107 -4.842 54.302 1.00
20.01 C
HETATM 2423 O5' 3DR B 6 59.337 -5.867 55.258 1.00
16.98 O
-Eric
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