Messages

1

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: July 23, 2021, 05:56:15 pm »

And also it print lots of warning messages during the run.
I can't locate the origin of this warning.



Time used: 00:00:00:00
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'

Processing file '/tmp/tmpinhy880j.pdb'
   more than one < P  > atoms in J.DG56
   *****the first match is used*****
   more than one < OP1> atoms in J.DG56
   *****the first match is used*****
   more than one < OP2> atoms in J.DG56
   *****the first match is used*****
   more than one < O5'> atoms in J.DG56
   *****the first match is used*****
   more than one < C5'> atoms in J.DG56
   *****the first match is used*****
   more than one < C4'> atoms in J.DG56
   *****the first match is used*****
   more than one < O4'> atoms in J.DG56
   *****the first match is used*****
   more than one < C3'> atoms in J.DG56
   *****the first match is used*****
   more than one < O3'> atoms in J.DG56
   *****the first match is used*****
   more than one < C2'> atoms in J.DG56
   *****the first match is used*****
   more than one < C1'> atoms in J.DG56
   *****the first match is used*****
   more than one < N9 > atoms in J.DG56
   *****the first match is used*****
   more than one < C4 > atoms in J.DG56
   *****the first match is used*****
   more than one < C8 > atoms in J.DG56
   *****the first match is used*****

2

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: July 23, 2021, 05:54:17 pm »

Thank you so much for helpful information!

Yes, I tried and finally manage to color differently at each nucleotide blocks.
But it is quite slow since it make all individual block object for every nucleotide.

Do you have any suggest to do this more efficient way?


This is pml code I used to do this.

reinitialize
fetch 5O9G
hide all

create protein, chain A+C+B+E+D+G+F+H+W
set cartoon_color, purpleblue, protein
set cartoon_transparency, 0.6889, protein
show cartoon, protein

create na_I, chain I
set cartoon_nucleic_acid_color, red, na_I
show cartoon, na_I

create na_J, chain J
set cartoon_nucleic_acid_color, green, na_J
show cartoon, na_J

select C3_prime, name C3'
show sphere, C3_prime
set sphere_scale, 0.2, C3_prime
color gray90, C3_prime

set cartoon_ladder_mode, 1
set cartoon_ladder_radius, 0.1
set cartoon_ladder_color, black

set cartoon_tube_radius, 0.16889
set cartoon_nucleic_acid_mode, 1

dssr_block (chain I and resi 0), block_color='N:[0.0 0.3 1.0]'
dssr_block (chain I and resi 1), block_color='N:[0.0 0.786 1.0]'
dssr_block (chain I and resi 2), block_color='N:[0.123 1.0 0.844]'
dssr_block (chain I and resi 3), block_color='N:[0.781 1.0 0.187]'
dssr_block (chain I and resi 4), block_color='N:[0.642 1.0 0.326]'
dssr_block (chain I and resi 5), block_color='N:[0.0 0.0 0.536]'
dssr_block (chain I and resi 6), block_color='N:[1.0 0.887 0.0]'
dssr_block (chain I and resi 7), block_color='N:[0.313 1.0 0.655]'
dssr_block (chain I and resi , block_color='N:[0.0 0.692 1.0]'
dssr_block (chain I and resi 9), block_color='N:[1.0 0.175 0.0]'
dssr_block (chain I and resi 10), block_color='N:[1.0 0.393 0.0]'
dssr_block (chain I and resi 11), block_color='N:[0.047 0.959 0.92]'
dssr_block (chain I and resi 12), block_color='N:[0.0 0.724 1.0]'
dssr_block (chain I and resi 13), block_color='N:[0.212 1.0 0.756]'
dssr_block (chain I and resi 14), block_color='N:[1.0 0.727 0.0]'
dssr_block (chain I and resi 15), block_color='N:[0.0 0.0 0.678]'
dssr_block (chain I and resi 16), block_color='N:[0.66 0.0 0.0]'
dssr_block (chain I and resi 17), block_color='N:[0.0 0.316 1.0]'
dssr_block (chain I and resi 18), block_color='N:[0.0 0.0 0.536]'
dssr_block (chain I and resi 19), block_color='N:[0.0 0.0 0.732]'
dssr_block (chain I and resi 20), block_color='N:[0.0 0.0 0.785]'
dssr_block (chain I and resi 21), block_color='N:[0.0 0.206 1.0]'
dssr_block (chain I and resi 22), block_color='N:[0.0 0.535 1.0]'
dssr_block (chain I and resi 23), block_color='N:[1.0 0.291 0.0]'
dssr_block (chain I and resi 24), block_color='N:[1.0 0.349 0.0]'
dssr_block (chain I and resi 25), block_color='N:[0.839 0.0 0.0]'
dssr_block (chain I and resi 26), block_color='N:[0.0 0.755 1.0]'
dssr_block (chain I and resi 27), block_color='N:[0.693 1.0 0.275]'
dssr_block (chain I and resi 28), block_color='N:[0.0 0.363 1.0]'
dssr_block (chain I and resi 29), block_color='N:[0.0 0.331 1.0]'
dssr_block (chain I and resi 30), block_color='N:[0.821 0.0 0.0]'
dssr_block (chain I and resi 31), block_color='N:[1.0 0.625 0.0]'
dssr_block (chain I and resi 32), block_color='N:[0.0 0.457 1.0]'
dssr_block (chain I and resi 33), block_color='N:[0.262 1.0 0.705]'
dssr_block (chain I and resi 34), block_color='N:[0.0 0.598 1.0]'
dssr_block (chain I and resi 35), block_color='N:[1.0 0.669 0.0]'
dssr_block (chain I and resi 36), block_color='N:[1.0 0.088 0.0]'
dssr_block (chain I and resi 37), block_color='N:[0.0 0.786 1.0]'
dssr_block (chain I and resi 38), block_color='N:[0.553 1.0 0.414]'
dssr_block (chain I and resi 39), block_color='N:[1.0 0.669 0.0]'
dssr_block (chain I and resi 40), block_color='N:[0.0 0.0 0.536]'
dssr_block (chain I and resi 41), block_color='N:[1.0 0.582 0.0]'
dssr_block (chain I and resi 42), block_color='N:[0.338 1.0 0.629]'
dssr_block (chain I and resi 43), block_color='N:[0.0 0.065 1.0]'
dssr_block (chain I and resi 44), block_color='N:[1.0 0.48 0.0]'
dssr_block (chain I and resi 45), block_color='N:[0.0 0.849 1.0]'
dssr_block (chain I and resi 46), block_color='N:[0.541 1.0 0.427]'
dssr_block (chain I and resi 47), block_color='N:[0.0 0.849 1.0]'
dssr_block (chain I and resi 48), block_color='N:[1.0 0.901 0.0]'
dssr_block (chain I and resi 49), block_color='N:[0.0 0.033 1.0]'
dssr_block (chain I and resi 50), block_color='N:[0.0 0.018 1.0]'
dssr_block (chain I and resi 51), block_color='N:[0.0 0.065 1.0]'
dssr_block (chain I and resi 52), block_color='N:[1.0 0.872 0.0]'
dssr_block (chain I and resi 53), block_color='N:[0.756 1.0 0.212]'
dssr_block (chain I and resi 54), block_color='N:[0.0 0.0 0.999]'
dssr_block (chain I and resi 55), block_color='N:[0.731 1.0 0.237]'
dssr_block (chain I and resi 56), block_color='N:[0.0 0.049 1.0]'
dssr_block (chain I and resi 57), block_color='N:[0.0 0.676 1.0]'
dssr_block (chain I and resi 58), block_color='N:[0.0 0.0 0.625]'
dssr_block (chain I and resi 59), block_color='N:[0.963 0.044 0.0]'
dssr_block (chain I and resi 60), block_color='N:[1.0 0.335 0.0]'
dssr_block (chain I and resi 61), block_color='N:[0.073 0.99 0.895]'
dssr_block (chain I and resi 62), block_color='N:[0.92 1.0 0.047]'
dssr_block (chain I and resi 63), block_color='N:[0.351 1.0 0.617]'
dssr_block (chain I and resi 64), block_color='N:[0.225 1.0 0.743]'
dssr_block (chain I and resi 65), block_color='N:[0.528 1.0 0.44]'
dssr_block (chain I and resi 66), block_color='N:[0.022 0.927 0.946]'
dssr_block (chain I and resi 67), block_color='N:[1.0 0.814 0.0]'
dssr_block (chain I and resi 68), block_color='N:[0.0 0.52 1.0]'
dssr_block (chain I and resi 69), block_color='N:[0.0 0.865 0.996]'
dssr_block (chain I and resi 70), block_color='N:[0.625 0.0 0.0]'
dssr_block (chain I and resi 71), block_color='N:[0.174 1.0 0.794]'
dssr_block (chain I and resi 72), block_color='N:[0.882 1.0 0.085]'
dssr_block (chain I and resi 73), block_color='N:[0.0 0.0 0.821]'
dssr_block (chain I and resi 74), block_color='N:[0.0 0.488 1.0]'
dssr_block (chain I and resi 75), block_color='N:[0.553 0.0 0.0]'
dssr_block (chain I and resi 76), block_color='N:[0.0 0.0 0.767]'
dssr_block (chain I and resi 77), block_color='N:[0.0 0.018 1.0]'
dssr_block (chain I and resi 78), block_color='N:[0.705 1.0 0.262]'
dssr_block (chain I and resi 79), block_color='N:[0.0 0.0 0.981]'
dssr_block (chain I and resi 80), block_color='N:[0.427 1.0 0.541]'
dssr_block (chain I and resi 81), block_color='N:[0.0 0.0 0.553]'
dssr_block (chain I and resi 82), block_color='N:[0.803 0.0 0.0]'
dssr_block (chain I and resi 83), block_color='N:[0.262 1.0 0.705]'
dssr_block (chain I and resi 84), block_color='N:[0.0 0.441 1.0]'
dssr_block (chain I and resi 85), block_color='N:[0.136 1.0 0.832]'
dssr_block (chain I and resi 86), block_color='N:[0.0 0.363 1.0]'
dssr_block (chain I and resi 87), block_color='N:[0.0 0.504 1.0]'
dssr_block (chain I and resi 88), block_color='N:[0.009 0.912 0.958]'
dssr_block (chain I and resi 89), block_color='N:[0.0 0.629 1.0]'
dssr_block (chain I and resi -2), block_color='N:[1.0 0.16 0.0]'
dssr_block (chain I and resi -72), block_color='N:[0.402 1.0 0.566]'
dssr_block (chain I and resi -71), block_color='N:[0.0 0.582 1.0]'
dssr_block (chain I and resi -70), block_color='N:[0.696 0.0 0.0]'
dssr_block (chain I and resi -69), block_color='N:[0.0 0.0 0.981]'
dssr_block (chain I and resi -68), block_color='N:[0.0 0.41 1.0]'
dssr_block (chain I and resi -67), block_color='N:[0.693 1.0 0.275]'
dssr_block (chain I and resi -66), block_color='N:[0.0 0.018 1.0]'
dssr_block (chain I and resi -65), block_color='N:[0.022 0.927 0.946]'
dssr_block (chain I and resi -64), block_color='N:[0.047 0.959 0.92]'
dssr_block (chain I and resi -63), block_color='N:[0.806 1.0 0.161]'
dssr_block (chain I and resi -62), block_color='N:[0.718 1.0 0.25]'
dssr_block (chain I and resi -61), block_color='N:[0.0 0.0 0.803]'
dssr_block (chain I and resi -60), block_color='N:[1.0 0.204 0.0]'
dssr_block (chain I and resi -59), block_color='N:[0.819 1.0 0.149]'
dssr_block (chain I and resi -58), block_color='N:[0.553 0.0 0.0]'
dssr_block (chain I and resi -57), block_color='N:[0.465 1.0 0.503]'
dssr_block (chain I and resi -56), block_color='N:[1.0 0.771 0.0]'
dssr_block (chain I and resi -55), block_color='N:[1.0 0.422 0.0]'
dssr_block (chain I and resi -54), block_color='N:[0.0 0.504 1.0]'
dssr_block (chain I and resi -53), block_color='N:[0.0 0.0 0.696]'
dssr_block (chain I and resi -52), block_color='N:[0.971 0.959 0.0]'
dssr_block (chain I and resi -51), block_color='N:[0.642 1.0 0.326]'
dssr_block (chain I and resi -50), block_color='N:[1.0 0.248 0.0]'
dssr_block (chain I and resi -49), block_color='N:[0.0 0.833 1.0]'
dssr_block (chain I and resi -48), block_color='N:[0.536 0.0 0.0]'
dssr_block (chain I and resi -47), block_color='N:[0.0 0.0 0.981]'
dssr_block (chain I and resi -46), block_color='N:[1.0 0.901 0.0]'
dssr_block (chain I and resi -45), block_color='N:[0.44 1.0 0.528]'
dssr_block (chain I and resi -44), block_color='N:[0.0 0.175 1.0]'
dssr_block (chain I and resi -43), block_color='N:[0.0 0.645 1.0]'
dssr_block (chain I and resi -42), block_color='N:[0.642 1.0 0.326]'
dssr_block (chain I and resi -41), block_color='N:[0.571 0.0 0.0]'
dssr_block (chain I and resi -40), block_color='N:[1.0 0.814 0.0]'
dssr_block (chain I and resi -39), block_color='N:[0.0 0.708 1.0]'
dssr_block (chain I and resi -38), block_color='N:[0.225 1.0 0.743]'
dssr_block (chain I and resi -37), block_color='N:[0.0 0.567 1.0]'
dssr_block (chain I and resi -36), block_color='N:[0.87 1.0 0.098]'
dssr_block (chain I and resi -35), block_color='N:[0.971 0.959 0.0]'
dssr_block (chain I and resi -34), block_color='N:[0.199 1.0 0.769]'
dssr_block (chain I and resi -33), block_color='N:[0.136 1.0 0.832]'
dssr_block (chain I and resi -32), block_color='N:[1.0 0.712 0.0]'
dssr_block (chain I and resi -31), block_color='N:[1.0 0.436 0.0]'
dssr_block (chain I and resi -30), block_color='N:[0.767 0.0 0.0]'
dssr_block (chain I and resi -29), block_color='N:[0.0 0.0 0.946]'
dssr_block (chain I and resi -28), block_color='N:[0.262 1.0 0.705]'
dssr_block (chain I and resi -27), block_color='N:[0.553 0.0 0.0]'
dssr_block (chain I and resi -26), block_color='N:[0.92 1.0 0.047]'
dssr_block (chain I and resi -25), block_color='N:[0.478 1.0 0.49]'
dssr_block (chain I and resi -24), block_color='N:[0.0 0.0 0.732]'
dssr_block (chain I and resi -23), block_color='N:[0.009 0.912 0.958]'
dssr_block (chain I and resi -22), block_color='N:[0.478 1.0 0.49]'
dssr_block (chain I and resi -21), block_color='N:[0.882 1.0 0.085]'
dssr_block (chain I and resi -20), block_color='N:[0.0 0.112 1.0]'
dssr_block (chain I and resi -19), block_color='N:[0.3 1.0 0.667]'
dssr_block (chain I and resi -18), block_color='N:[0.0 0.441 1.0]'
dssr_block (chain I and resi -17), block_color='N:[0.0 0.127 1.0]'
dssr_block (chain I and resi -16), block_color='N:[0.981 0.059 0.0]'
dssr_block (chain I and resi -15), block_color='N:[0.06 0.975 0.908]'
dssr_block (chain I and resi -14), block_color='N:[0.0 0.645 1.0]'
dssr_block (chain I and resi -13), block_color='N:[0.0 0.425 1.0]'
dssr_block (chain I and resi -12), block_color='N:[0.0 0.237 1.0]'
dssr_block (chain I and resi -11), block_color='N:[0.136 1.0 0.832]'
dssr_block (chain I and resi -10), block_color='N:[1.0 0.8 0.0]'
dssr_block (chain I and resi -9), block_color='N:[0.364 1.0 0.604]'
dssr_block (chain I and resi -8), block_color='N:[0.0 0.033 1.0]'
dssr_block (chain I and resi -7), block_color='N:[1.0 0.8 0.0]'
dssr_block (chain I and resi -6), block_color='N:[0.895 1.0 0.073]'
dssr_block (chain I and resi -5), block_color='N:[0.0 0.0 0.518]'
dssr_block (chain I and resi -4), block_color='N:[0.667 1.0 0.3]'
dssr_block (chain I and resi -3), block_color='N:[0.91 0.001 0.0]'
dssr_block (chain I and resi -1), block_color='N:[1.0 0.32 0.0]'

dssr_block (chain J and resi 0), block_color='N:[0.0 0.159 1.0]'
dssr_block (chain J and resi 1), block_color='N:[0.427 1.0 0.541]'
dssr_block (chain J and resi 2), block_color='N:[1.0 0.422 0.0]'
dssr_block (chain J and resi 3), block_color='N:[1.0 0.291 0.0]'
dssr_block (chain J and resi 4), block_color='N:[0.0 0.645 1.0]'
dssr_block (chain J and resi 5), block_color='N:[1.0 0.175 0.0]'
dssr_block (chain J and resi 6), block_color='N:[0.629 1.0 0.338]'
dssr_block (chain J and resi 7), block_color='N:[0.794 1.0 0.174]'
dssr_block (chain J and resi , block_color='N:[0.0 0.676 1.0]'
dssr_block (chain J and resi 9), block_color='N:[1.0 0.858 0.0]'
dssr_block (chain J and resi 10), block_color='N:[0.0 0.535 1.0]'
dssr_block (chain J and resi 11), block_color='N:[1.0 0.277 0.0]'
dssr_block (chain J and resi 12), block_color='N:[0.0 0.52 1.0]'
dssr_block (chain J and resi 13), block_color='N:[0.174 1.0 0.794]'
dssr_block (chain J and resi 14), block_color='N:[0.376 1.0 0.591]'
dssr_block (chain J and resi 15), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi 16), block_color='N:[0.0 0.0 0.518]'
dssr_block (chain J and resi 17), block_color='N:[0.892 0.0 0.0]'
dssr_block (chain J and resi 18), block_color='N:[0.174 1.0 0.794]'
dssr_block (chain J and resi 19), block_color='N:[0.0 0.159 1.0]'
dssr_block (chain J and resi 20), block_color='N:[0.0 0.0 0.536]'
dssr_block (chain J and resi 21), block_color='N:[0.0 0.394 1.0]'
dssr_block (chain J and resi 22), block_color='N:[0.073 0.99 0.895]'
dssr_block (chain J and resi 23), block_color='N:[0.571 0.0 0.0]'
dssr_block (chain J and resi 24), block_color='N:[0.908 1.0 0.06]'
dssr_block (chain J and resi 25), block_color='N:[0.958 0.974 0.009]'
dssr_block (chain J and resi 26), block_color='N:[0.963 0.044 0.0]'
dssr_block (chain J and resi 27), block_color='N:[0.821 0.0 0.0]'
dssr_block (chain J and resi 28), block_color='N:[0.136 1.0 0.832]'
dssr_block (chain J and resi 29), block_color='N:[0.0 0.488 1.0]'
dssr_block (chain J and resi 30), block_color='N:[0.0 0.159 1.0]'
dssr_block (chain J and resi 31), block_color='N:[0.693 1.0 0.275]'
dssr_block (chain J and resi 32), block_color='N:[1.0 0.451 0.0]'
dssr_block (chain J and resi 33), block_color='N:[0.0 0.629 1.0]'
dssr_block (chain J and resi 34), block_color='N:[0.999 0.073 0.0]'
dssr_block (chain J and resi 35), block_color='N:[0.0 0.896 0.971]'
dssr_block (chain J and resi 36), block_color='N:[0.832 1.0 0.136]'
dssr_block (chain J and resi 37), block_color='N:[0.0 0.0 0.5]'
dssr_block (chain J and resi 38), block_color='N:[0.625 0.0 0.0]'
dssr_block (chain J and resi 39), block_color='N:[0.0 0.0 0.5]'
dssr_block (chain J and resi 40), block_color='N:[0.0 0.818 1.0]'
dssr_block (chain J and resi 41), block_color='N:[0.553 1.0 0.414]'
dssr_block (chain J and resi 42), block_color='N:[0.0 0.253 1.0]'
dssr_block (chain J and resi 43), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi 44), block_color='N:[0.503 1.0 0.465]'
dssr_block (chain J and resi 45), block_color='N:[0.0 0.316 1.0]'
dssr_block (chain J and resi 46), block_color='N:[0.035 0.943 0.933]'
dssr_block (chain J and resi 47), block_color='N:[0.389 1.0 0.579]'
dssr_block (chain J and resi 48), block_color='N:[0.731 1.0 0.237]'
dssr_block (chain J and resi 49), block_color='N:[0.874 0.0 0.0]'
dssr_block (chain J and resi 50), block_color='N:[0.528 1.0 0.44]'
dssr_block (chain J and resi 51), block_color='N:[0.0 0.0 0.981]'
dssr_block (chain J and resi 52), block_color='N:[1.0 0.291 0.0]'
dssr_block (chain J and resi 53), block_color='N:[0.503 1.0 0.465]'
dssr_block (chain J and resi 54), block_color='N:[0.655 1.0 0.313]'
dssr_block (chain J and resi 55), block_color='N:[0.0 0.0 0.767]'
dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'
dssr_block (chain J and resi 57), block_color='N:[0.389 1.0 0.579]'
dssr_block (chain J and resi 58), block_color='N:[0.667 1.0 0.3]'
dssr_block (chain J and resi 59), block_color='N:[1.0 0.175 0.0]'
dssr_block (chain J and resi 60), block_color='N:[0.769 1.0 0.199]'
dssr_block (chain J and resi 61), block_color='N:[0.288 1.0 0.68]'
dssr_block (chain J and resi 62), block_color='N:[0.731 1.0 0.237]'
dssr_block (chain J and resi 63), block_color='N:[0.0 0.0 0.732]'
dssr_block (chain J and resi 64), block_color='N:[0.68 1.0 0.288]'
dssr_block (chain J and resi 65), block_color='N:[0.161 1.0 0.806]'
dssr_block (chain J and resi 66), block_color='N:[0.0 0.896 0.971]'
dssr_block (chain J and resi 67), block_color='N:[0.3 1.0 0.667]'
dssr_block (chain J and resi 68), block_color='N:[0.693 1.0 0.275]'
dssr_block (chain J and resi 69), block_color='N:[0.0 0.833 1.0]'
dssr_block (chain J and resi 70), block_color='N:[0.0 0.441 1.0]'
dssr_block (chain J and resi 71), block_color='N:[1.0 0.248 0.0]'
dssr_block (chain J and resi 72), block_color='N:[0.629 1.0 0.338]'
dssr_block (chain J and resi -1), block_color='N:[0.91 0.001 0.0]'
dssr_block (chain J and resi -89), block_color='N:[0.882 1.0 0.085]'
dssr_block (chain J and resi -88), block_color='N:[0.0 0.08 1.0]'
dssr_block (chain J and resi -87), block_color='N:[0.111 1.0 0.857]'
dssr_block (chain J and resi -86), block_color='N:[0.0 0.739 1.0]'
dssr_block (chain J and resi -85), block_color='N:[0.617 1.0 0.351]'
dssr_block (chain J and resi -84), block_color='N:[0.0 0.0 0.571]'
dssr_block (chain J and resi -83), block_color='N:[1.0 0.538 0.0]'
dssr_block (chain J and resi -82), block_color='N:[0.0 0.0 0.714]'
dssr_block (chain J and resi -81), block_color='N:[0.0 0.582 1.0]'
dssr_block (chain J and resi -80), block_color='N:[0.0 0.567 1.0]'
dssr_block (chain J and resi -79), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi -78), block_color='N:[0.0 0.865 0.996]'
dssr_block (chain J and resi -77), block_color='N:[0.91 0.001 0.0]'
dssr_block (chain J and resi -76), block_color='N:[0.806 1.0 0.161]'
dssr_block (chain J and resi -75), block_color='N:[0.414 1.0 0.553]'
dssr_block (chain J and resi -74), block_color='N:[0.0 0.0 0.839]'
dssr_block (chain J and resi -73), block_color='N:[0.0 0.0 0.696]'
dssr_block (chain J and resi -72), block_color='N:[0.0 0.316 1.0]'
dssr_block (chain J and resi -71), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi -70), block_color='N:[1.0 0.306 0.0]'
dssr_block (chain J and resi -69), block_color='N:[0.0 0.0 0.553]'
dssr_block (chain J and resi -68), block_color='N:[0.0 0.52 1.0]'
dssr_block (chain J and resi -67), block_color='N:[1.0 0.916 0.0]'
dssr_block (chain J and resi -66), block_color='N:[0.0 0.378 1.0]'
dssr_block (chain J and resi -65), block_color='N:[0.839 0.0 0.0]'
dssr_block (chain J and resi -64), block_color='N:[0.5 0.0 0.0]'
dssr_block (chain J and resi -63), block_color='N:[0.161 1.0 0.806]'
dssr_block (chain J and resi -62), block_color='N:[1.0 0.901 0.0]'
dssr_block (chain J and resi -61), block_color='N:[1.0 0.436 0.0]'
dssr_block (chain J and resi -60), block_color='N:[0.0 0.143 1.0]'
dssr_block (chain J and resi -59), block_color='N:[0.0 0.0 0.821]'
dssr_block (chain J and resi -58), block_color='N:[0.0 0.786 1.0]'
dssr_block (chain J and resi -57), block_color='N:[0.0 0.284 1.0]'
dssr_block (chain J and resi -56), block_color='N:[0.009 0.912 0.958]'
dssr_block (chain J and resi -55), block_color='N:[1.0 0.8 0.0]'
dssr_block (chain J and resi -54), block_color='N:[0.0 0.0 0.589]'
dssr_block (chain J and resi -53), block_color='N:[1.0 0.611 0.0]'
dssr_block (chain J and resi -52), block_color='N:[0.625 0.0 0.0]'
dssr_block (chain J and resi -51), block_color='N:[1.0 0.146 0.0]'
dssr_block (chain J and resi -50), block_color='N:[0.767 0.0 0.0]'
dssr_block (chain J and resi -49), block_color='N:[1.0 0.131 0.0]'
dssr_block (chain J and resi -48), block_color='N:[0.0 0.0 0.999]'
dssr_block (chain J and resi -47), block_color='N:[0.212 1.0 0.756]'
dssr_block (chain J and resi -46), block_color='N:[0.0 0.0 0.857]'
dssr_block (chain J and resi -45), block_color='N:[0.503 1.0 0.465]'
dssr_block (chain J and resi -44), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi -43), block_color='N:[0.0 0.0 0.625]'
dssr_block (chain J and resi -42), block_color='N:[0.123 1.0 0.844]'
dssr_block (chain J and resi -41), block_color='N:[0.678 0.0 0.0]'
dssr_block (chain J and resi -40), block_color='N:[1.0 0.814 0.0]'
dssr_block (chain J and resi -39), block_color='N:[1.0 0.538 0.0]'
dssr_block (chain J and resi -38), block_color='N:[0.0 0.096 1.0]'
dssr_block (chain J and resi -37), block_color='N:[1.0 0.277 0.0]'
dssr_block (chain J and resi -36), block_color='N:[0.149 1.0 0.819]'
dssr_block (chain J and resi -35), block_color='N:[0.0 0.786 1.0]'
dssr_block (chain J and resi -34), block_color='N:[0.731 1.0 0.237]'
dssr_block (chain J and resi -33), block_color='N:[0.0 0.708 1.0]'
dssr_block (chain J and resi -32), block_color='N:[1.0 0.683 0.0]'
dssr_block (chain J and resi -31), block_color='N:[0.819 1.0 0.149]'
dssr_block (chain J and resi -30), block_color='N:[1.0 0.843 0.0]'
dssr_block (chain J and resi -29), block_color='N:[1.0 0.8 0.0]'
dssr_block (chain J and resi -28), block_color='N:[0.66 0.0 0.0]'
dssr_block (chain J and resi -27), block_color='N:[0.3 1.0 0.667]'
dssr_block (chain J and resi -26), block_color='N:[1.0 0.901 0.0]'
dssr_block (chain J and resi -25), block_color='N:[0.0 0.425 1.0]'
dssr_block (chain J and resi -24), block_color='N:[0.0 0.0 0.839]'
dssr_block (chain J and resi -23), block_color='N:[0.0 0.504 1.0]'
dssr_block (chain J and resi -22), block_color='N:[0.769 1.0 0.199]'
dssr_block (chain J and resi -21), block_color='N:[0.0 0.0 0.518]'
dssr_block (chain J and resi -20), block_color='N:[0.0 0.629 1.0]'
dssr_block (chain J and resi -19), block_color='N:[1.0 0.204 0.0]'
dssr_block (chain J and resi -18), block_color='N:[0.0 0.441 1.0]'
dssr_block (chain J and resi -17), block_color='N:[0.035 0.943 0.933]'
dssr_block (chain J and resi -16), block_color='N:[0.874 0.0 0.0]'
dssr_block (chain J and resi -15), block_color='N:[0.0 0.802 1.0]'
dssr_block (chain J and resi -14), block_color='N:[0.928 0.015 0.0]'
dssr_block (chain J and resi -13), block_color='N:[0.3 1.0 0.667]'
dssr_block (chain J and resi -12), block_color='N:[1.0 0.756 0.0]'
dssr_block (chain J and resi -11), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi -10), block_color='N:[0.92 1.0 0.047]'
dssr_block (chain J and resi -9), block_color='N:[0.0 0.08 1.0]'
dssr_block (chain J and resi -8), block_color='N:[0.009 0.912 0.958]'
dssr_block (chain J and resi -7), block_color='N:[0.882 1.0 0.085]'
dssr_block (chain J and resi -6), block_color='N:[0.262 1.0 0.705]'
dssr_block (chain J and resi -5), block_color='N:[0.0 0.0 0.643]'
dssr_block (chain J and resi -4), block_color='N:[0.0 0.378 1.0]'
dssr_block (chain J and resi -3), block_color='N:[1.0 0.814 0.0]'
dssr_block (chain J and resi -2), block_color='N:[0.642 1.0 0.326]'

bg_color white
remove solvent
hide everything, hydro

util.cbaw
set sphere_quality, 4
set stick_quality, 16

set depth_cue, 0
set ray_trace_fog, 0

set ray_shadow, off
set orthoscopic, 1

set antialias, 1
set valence, 0

set ambient, 0.68
set reflect, 0
set direct, 0.6
set spec_direct, 0
set light_count, 1

zoom complete=1
ray 1800
png 5O9G_test_block.png

3

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: July 09, 2021, 03:33:40 pm »

And manual selection of a particular nucleotide in particular position didn't help as I post i the earlier thread:
It only change the color of real nucleotide in the block not the block itself....

4

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: July 09, 2021, 03:30:09 pm »

Thank you for your kind answer!

Yes, I understood the color-option in the article but this setting will color "all" nucleotide of same kinds into a single color.
For example, color all Guanine by yellow.

But I want to do this:
color G at position 4 by yellow but Gs at position 5, 10, 11 by blue, etc

Do you have any idea to do that?

5

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: May 27, 2021, 02:41:46 pm »

Thank you so much for reply!

Here is example,

I made block image of pdb file:
x3dna-dssr -i=6rjg.pdb --blocview=png-c3 --block-file=wc-minor -o=6rjg.pml

I loaded pml file and I selected one nucleotide in pymol as figure I attached.
And type "color red, sele" to change the block color from blue to red.

But the block color (which I selected) is not changed, but I think the color of nucleotide embedded in the block is changed instead.
Do you have any suggestion to change the color of particular block of nucleotide which I selected?

Thanks

6

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: May 27, 2021, 02:40:11 pm »

Thank you so much for reply!

Here is example,

I made block image of pdb file:
x3dna-dssr -i=6rjg.pdb --blocview=png-c3 --block-file=wc-minor -o=6rjg.pml

I loaded pml file and I selected one nucleotide in pymol as figure I attached.
And type "color red, sele" to change the block color from blue to red.

But the block color (which I selected) is not changed, but I think the color of nucleotide embedded in the block is changed instead.
Do you have any suggestion to change the color of particular block of nucleotide which I selected?

Thanks

7

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: May 26, 2021, 04:23:47 pm »

I tried it in pymol, but only the color of real nucleotide was changed, not the color of "block".

8

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: May 26, 2021, 04:19:42 pm »

Thanks for reply!

Could I know how to do in pymol-plugin ?

9

RNA structures (DSSR) / Color each block nucleotide at each locations

« on: May 26, 2021, 03:43:15 pm »

I know I can color according to nucleotide type (like A, T, C, G).
But is it possible to color each block nucleotide at different location with different user-defined color?

For example,
nucleotide at residue 1 -> yellow
nucleotide at residue 2 -> purple, etc