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61

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

« Last post by xiangjun on July 23, 2021, 06:17:33 pm »

Yes, I tried and finally manage to color differently at each nucleotide blocks.

Glad to know that you have managed to color nucleotide blocks as desired. This is an important first step for later on speed optimizations.

But it is quite slow since it make all individual block object for every nucleotide.

How many colors do you want to have? Grouping nucleotides with the same color should speed up the process. It is now a matter of PyMOL selection syntax to play with.

And also it print lots of warning messages during the run.
I can't locate the origin of this warning.
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'

I cannot reproduce the warning messages. Let's not worry about them right now.

Best regards,

Xiang-Jun

62

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

« Last post by spark159 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*****

63

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

« Last post by spark159 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

64

Bug reports / Re: Uncaught exception error

« Last post by xiangjun on July 21, 2021, 09:50:10 pm »

Hi,

The DSSR version you used is v1.9.4-2019jul08. The latest DSSR version is v2.3.2-2021jun29, which works as expected for PDB entry 6jwe, as shown below:

Code: [Select]

x3dna-dssr --more --loop=with-stems --json -i=6jwe.pdb -o=6jwe.json

Processing file '6jwe.pdb'
    total number of nucleotides: 20
    total number of base pairs: 18
    total number of helices: 2
    total number of multiplets: 4
    total number of atom-base capping interactions: 2
    total number of splayed-apart dinucleotides: 2
    total number of non-loop single-stranded segments: 1
    total number of G-tetrads: 3
    total number of G4-helices: 1
    total number of G4-stems: 1
So please update your DSSR to the latest version (available exclusively from Columbia Technology Ventures).

Best regards,

Xiang-Jun

65

Bug reports / Uncaught exception error

« Last post by sgu0752 on July 21, 2021, 08:54:34 pm »

Hi xiangjun,

I use v1.9.4-2019jul08 of 3DNA-DSSR to analyze PDB structures, and I encountered an error looking at a relatively recent NMR structure 6jwe.

Code: [Select]

x3dna-dssr --more --loop=with-stems --json -i=6jwe.pdb -o=6jwe.json
Processing file ‘6jwe.pdb’
  total number of nucleotides: 20
  total number of base pairs: 18
Uncaught exception ‘Assertion failed’ raised at [fncs_hbond.c:826]
aborting...
Thanks in advance!

66

RNA structures (DSSR) / Re: Removing some nucleotides and fixing/reducing the loop in my RNA structure

« Last post by Sruthi0412 on July 20, 2021, 06:21:06 am »

This is an already existing crystal structure sequence upon which we are going to do some molecular dynamics simulations. The given RNA structure interacts with a protein as well. We are trying to establish the effect in protein dynamics and conformations upon shortening our RNA structure. Experimentally the underlines sequences have been removed and studies have been performed. The computational modelling also should be done in a similar methodology. Therefore I want to know if such removal of basepairs and adjusting the loops is possible, taking an existing crystal structure pdb.
5'-GUUUUAGAGCUAUGCUGAAAAGCAUAGCUCUAAAAC-3'

67

RNA structures (DSSR) / Re: Classical RNA loop motifs

« Last post by xiangjun on July 19, 2021, 08:49:19 am »

Hi Dr. Baulin,

As I understand correctly, for the moment there is no program (or database) that annotates (or stores) classical RNA loop motifs explicitly.
By the classical RNA loop motifs I mean sarcin/ricin loop, E-loop, tandem sheared G-A, GA/AAG internal loop, UAA/GAN internal loop, kink-turn, etc.

You may be right. Your list of 'classical RNA loop motifs' includes `etc.` and I am not sure/aware of the complete list.

As I know it:
1) only kink-turns are annotated by DSSR.

DSSR isn't intended to be a comprehensive tool for annotating 'classical RNA loop motifs.' DSSR, on the other hand, includes the fundamentals (such as base-pairing/stacking annotations and backbone torsions) that should make any downstream pipeline easier to annotate any well-defined RNA structural motifs.

DSSR can auto-detect kink-turns because K-turns have striking structural features and important functional roles, and I want to have a thorough understanding of the motif. Personally, I've found that only by implementing a topic/concept in detail source code can I truly comprehend it.

The Tamar Schlick made use of this DSSR features in their 2017 NAR paper "Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction." Please take a look at the following two threads (which also demonstrate the value of the 3DNA Forum) initiated by lead author of the paper:

• "Bending angle of internal loops"
• "1MZP"

2) for sarcin/ricin loop, E-loop, and tandem sheared G-A the best way of annotation is to use manually curated annotation from RNAMotifContrast and merge it with the RNA Motif Atlas clusters' identifiers.

RNAMotifContrast and RNA Motif Atlas clusters are certainly well-known resources on the topic. Another source of information that is worth checking is the Janusz Bujnicki lab website.

3) for GA/AAG internal loop and UAA/GAN internal loop annotation there are no existing ways at all.

DSSR has a dedicated section of ALL internal loops. Filtered by sequence constraints and geometric constraints, you might find what you're looking for.

If I'm wrong, could you please let me know if I missed anything?
If I'm right, are there any plans to add the mentioned motifs to DSSR functionality in the future?

In the future, I may add more motif annotations to DSSR Pro.

Best regards,

Xiang-Jun

68

RNA structures (DSSR) / Re: Removing some nucleotides and fixing/reducing the loop in my RNA structure

« Last post by xiangjun on July 19, 2021, 08:08:17 am »

In principle, I understand what you're trying to accomplish. However, I am unable to provide any concrete answers due to a lack of information.

69

RNA structures (DSSR) / Removing some nucleotides and fixing/reducing the loop in my RNA structure

« Last post by Sruthi0412 on July 19, 2021, 07:29:24 am »

I have an RNA sequence as below:
5'-GUUUUAGAGCUAUGCUGAAAAGCAUAGCUCUAAAAC-3'

In this, the bold region forms a loop. I want to remove the underlined base pairs( adjacent to the loop) and connect the loop to the rest of the system. In this way my system would be shorter. Is it possible to do such removal and fixing using 3DNA? Kindly guide regarding the same.
After removal my system should look like this

5'-GUUUUAGAGCUAUGAAAAUAGCUCUAAAAC-3'

70

RNA structures (DSSR) / Classical RNA loop motifs

« Last post by febos on July 19, 2021, 04:00:41 am »

Dear Dr. Lu,

As I understand correctly, for the moment there is no program (or database) that annotates (or stores) classical RNA loop motifs explicitly.
By the classical RNA loop motifs I mean sarcin/ricin loop, E-loop, tandem sheared G-A, GA/AAG internal loop, UAA/GAN internal loop, kink-turn, etc.

As I know it:
1) only kink-turns are annotated by DSSR.
2) for sarcin/ricin loop, E-loop, and tandem sheared G-A the best way of annotation is to use manually curated annotation from RNAMotifContrast and merge it with the RNA Motif Atlas clusters' identifiers.
3) for GA/AAG internal loop and UAA/GAN internal loop annotation there are no existing ways at all.

If I'm wrong, could you please let me know if I missed anything?
If I'm right, are there any plans to add the mentioned motifs to DSSR functionality in the future?

Thanks in advance!

Best regards,
Eugene Baulin