Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Recent Posts

Pages: 1 ... 8 9 [10]
91
I am currently working on a project that uses 1o15.pdb
It is a structure where RNA and theophylline molecules are bound. I want to mutate the bases of different sites of RNA at the same time.
For example, ACGUACGUACGU mutates positions 2-6 and mutates more than one base to ANNNNNGUACGU, and creates a new PDB file with 45 sequences. Can mutate_bases in X3DNA achieve this function?or it can use in dssr-basic. Thank you for your reply!

92
Hello! I would like to share with you some recent issues regarding the use of DSSR. First of all, thank you for your great contributions to DSSR and X3DNA, which have helped many scholars and are free for academic institutions to use. My question is as follows:
1. After I got the academic license through Columbia University, I downloaded two versions of dssr-basic for linux and windows. But the windows version of the exe installation package can't open all the time. I have tried it on several computers with win7 and win10, but it doesn't work, so I would like to ask Dr. Lu why.
2. The files in the linux installation package are not in tar.gz format. I don't know how to install it. Could you please tell me. Or is there an installation method I haven't found? I did find it for a long time. So please let me know, thank you very much.  :D


Best wishes
chen long
93
General discussions (Q&As) / 3DNA manual
« Last post by chenlong on July 28, 2021, 01:33:34 am »
Hello, can I get a  the operation manual of x3DNA, 2.4  WINDOW version? I find but no result in this forum,sorry .
94
RNA structures (DSSR) / Re: how to repair a DNA model
« Last post by xiangjun on July 27, 2021, 11:48:48 am »
Please provide some background info and a concrete example to illustrate unambiguously what you want to achieve.

Thanks,

Xiang-Jun
95
RNA structures (DSSR) / how to repair a DNA model
« Last post by Garyren on July 27, 2021, 11:20:38 am »
I have a DNA model, however there are many broken chains in this model. I wonder if your DSSR can repair the broken DNA model?

96
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by xiangjun on July 23, 2021, 06:17:33 pm »
Quote
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.

Quote
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.

Quote
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

97
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*****
98
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 8), 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 8), 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




99
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


100
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!
Pages: 1 ... 8 9 [10]

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.