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21
RNA structures (DSSR) / Re: List only base pairs in output
« Last post by xiangjun on July 26, 2018, 01:32:12 pm »
Try:

x3dna-dssr -i=1ehz.pdb --json | jq -c '.pairs[] | [.bp, .name]'

You would get:

Code: [Select]
["G-C","WC"]
["C-G","WC"]
["G-C","WC"]
["G-U","Wobble"]
["A-U","WC"]
["U-A","WC"]
["U-A","WC"]
["U-A","rHoogsteen"]
["U+A","--"]
["A+A","--"]
["g-C","WC"]
["g+G","--"]
["C-G","WC"]
["U-A","WC"]
["C-G","WC"]
["G+C","rWC"]
["u+U","--"]
["G+P","--"]
["G-C","WC"]
["G-g","--"]
["g-A","Imino"]
["C-G","WC"]
["C-G","WC"]
["A-U","WC"]
["G-c","WC"]
["A-P","--"]
["c-A","--"]
["U-A","--"]
["c-G","WC"]
["U-A","WC"]
["G-C","WC"]
["U-A","WC"]
["G-C","WC"]
["t-a","rHoogsteen"]

The jq utility program can be found on https://stedolan.github.io/jq/.

HTH,

Xiang-Jun
22
RNA structures (DSSR) / List only base pairs in output
« Last post by Llewellyn on July 26, 2018, 12:41:16 pm »
Is there a command to fetch only the base pairs in the output?

bp name
G-C WC
G-C WC
G-C WC
A-U WC
G-C WC
C-A --   
C-C --   
C-G WC
C-G WC
C-G WC
U-A WC
U-A WC
C-G WC
C-G WC
G-C WC
A-U WC       
23
Thanks for such a well-phrased question! Yes, 3DNA/DSSR has some utilities that may help in achieving your goal.

Quote
4JVH.pdb (QKI) http://www.rcsb.org/structure/4JVH has the RNA ACUAACAA and I need to trim that to _ACUAAC because that lines up the best with YNCURAY.  The underscore needs to be the C or T and to do that I need 3DNA to add the C or T to the 5' end of the ACUAAC.

I assume the conformation of the 5' C or T to be added is not defined, i.e. it can be any (reasonable) starting geometry. You could use frame_mol to set the ACUAAC fragment from 4JVH to be in the base reference of the first A. You can choose any (or your favorite) CA (or TA) dinucleotide from the PDB, and use the same frame_mol utility to reset it to the base reference frame of the ending A. Since both the ACUAAC fragment and the CA fragment share the same A base reference frame, you can overlay them together. With some manual editing, you should be able to get an approximate starting PDB structure with required RNA base sequence for your MD simulations.

Have a try and let me know if it works.

Xiang-Jun
24
Does 3DNA have a function to add a nucleotide to the 5' end of an RNA in a pdb file?

My project is to search the transcriptome for more sites that the RNA-binding proteins QKI and SF1 might compete.  We already know that they compete just upstream of Exon 12 of NUMB and if QKI wins it prevents SF1 from binding and prevents SF1 from recruiting the spliceosome there, so exon skipping of exon 12 happens.


I know the motif for the QKI dimer is NACUAAY-N(1-20)-UAAY and the motif for the SF1 monomer (it does not dimerize) is YNCURAY.  After I run molecular dynamics of QKI against the SF1 RNA motif I will compare the binding energies to see how well QKI binds against the SF1 motif to see how well QKI competes against SF1.

I have used 3DNA's mutate_bases in the past in this project, but now I need to add a C or T to the 5' end of the RNA bound to QKI, because 4JVH.pdb (QKI) http://www.rcsb.org/structure/4JVH has the RNA ACUAACAA and I need to trim that to _ACUAAC because that lines up the best with YNCURAY.  The underscore needs to be the C or T and to do that I need 3DNA to add the C or T to the 5' end of the ACUAAC.
25
Sorry for being late in responding to your follow-up post on June 22, 2018. I was on a trip to China for the whole month of June and slightly beyond, and I was constrained by my schedule and limited internet access.

Now back to your question, I am confused by what you mean by the following quantitative measures:

Quote
trying to classify structures as A ( 75-100 percent = A , 57/58- 75 percent = A-like , 43% - 58% = A to B)...
About 63 percent B so, B- Like...
9 percent A..?

The classification of a DNA dinucleotide step as A-, B- or TA-type is (mostly) based on Zp. See the 2000 A-DNA motif paper in JMB, and the 3DNA source code (ana_fncs.c) for further details.

Best regards,

Xiang-Jun
26
Hello.

I was wondering if you had a response regarding my post above.

Thanks.
27
Hello. Thank you for your responses.

I will clarify my questions to the best of my ability.

I am trying to classify structures as A ( 75-100 percent = A , 57/58- 75 percent = A-like , 43% - 58% = A to B)  ..in this manner. I was wondering if 3dna has a way of accomplishing this without me having to do it manually say for a database of 300 structures of DNA/DNA and RNA/RNA duplexes that I have created.

Examples: step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 GG/CC   -2.93    8.97    0.37   -3.31    8.93    0.93     B
   2 GT/AC   -3.35    9.11   -0.39   -4.65    9.11    0.27     B
   3 TG/CA   -2.75    8.65   -0.88    0.06    8.42   -2.19     B
   4 GC/GC   -3.75    8.88   -1.02   -4.46    8.86    1.15     B
   5 CA/TG   -2.21    8.39   -0.80    0.87    8.11   -2.24
   6 AA/TT   -3.16    8.72   -0.76   -3.15    8.69   -1.08     B
   7 AC/GT   -3.34    8.80    0.30   -4.58    8.79   -0.36     B
   8 CA/TG   -3.15    8.59    0.82   -5.42    7.85    3.62
   9 AA/TT   -3.40    8.91   -0.05   -5.18    8.77    1.57     B
  10 AA/TT   -2.85    9.21    0.49   -4.46    8.93    2.31     B
  11 AT/AT   -2.73    9.23    0.37   -5.90    8.10    4.48
  12 TT/AA   -3.06    8.49    0.75   -7.77    2.66    8.09
  13 TG/CA   -1.93    8.53   -1.20   -1.73    8.42    1.80
  14 GA/TC   -3.71    8.29   -1.70   -1.39    8.33   -1.77
  15 AT/AT   -3.33    8.91    0.01   -3.85    8.89   -0.62     B
  16 TA/TA   -3.07    8.68    0.30   -3.26    8.62   -1.09     B
  17 AA/TT   -3.23    8.99   -0.12   -3.62    8.93   -1.05     B
  18 AG/CT   -2.99    8.80   -0.12   -4.25    8.76    0.81     B
  19 GC/GC   -2.88    8.98   -0.05   -2.91    8.98   -0.13     B
  20 CA/TG    ---     ---     ---     ---     ---     ---     ---
  21 AA/TT    ---     ---     ---     ---     ---     ---     ---
  22 AT/AT   -1.31    5.67   -0.75   -1.12    5.67   -0.38
  23 TG/CA   -3.05    9.04   -0.43   -1.94    9.05   -0.15     B
  24 GC/GC   -3.22    9.12   -0.18   -3.87    9.12    0.02     B
  25 CT/AG   -3.15    8.71    0.12   -4.40    8.67    0.80     B
  26 TT/AA   -3.20    9.07   -0.14   -3.66    9.01   -1.00     B
  27 TT/AA   -3.31    9.00   -0.28   -4.03    9.00   -0.28     B
  28 TT/AA   -3.32    8.90   -0.38   -3.06    8.75   -1.69     B
  29 TT/AA   -2.84    8.83   -0.02   -2.70    8.77   -0.99     B
  30 TT/AA   -3.17    8.80   -0.39   -4.01    8.81   -0.16     B
  31 TG/CA   -2.68    8.86   -0.39   -2.17    8.73    1.56     B
  32 GG/CC   -2.62    8.93    0.55   -4.88    8.43    3.01
  33 GC/GC   -3.01    9.06    0.57   -4.46    8.93    1.66

About 63 percent B so, B- Like
Structure 1ihf.pdb



    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 Ug/gA   -0.59    1.90  -10.29   -1.26   -5.96   -8.21
   2 gg/gg   -0.03   11.87   -0.05   -0.04   11.87   -0.05
   3 gA/Ug    4.30    6.48    0.76    4.86    6.47    0.71
   4 AG/GU    ---     ---     ---     ---     ---     ---     ---
   5 GA/UG    ---     ---     ---     ---     ---     ---     ---
   6 AG/GU    ---     ---     ---     ---     ---     ---     ---
   7 GA/UG    0.91    7.95   -3.89    0.95    7.96   -3.89
   8 AU/AU    ---     ---     ---     ---     ---     ---     ---
   9 UG/GA    4.86   -3.16   -3.09    3.46   -5.61   -2.45
  10 GG/GG    2.86   -8.07    9.47    0.69  -11.79    7.22
  11 GU/UG   -0.70   -5.57    0.33   -0.39   -5.58   -0.02
  12 UA/UU    4.87    4.65    9.91    6.37    4.62    8.66
  13 Ag/gU    ---     ---     ---     ---     ---     ---     ---
  14 gU/Ag    ---     ---     ---     ---     ---     ---     ---
  15 UG/GA    4.76   -3.15   -3.07    3.40   -5.68   -2.41
  16 GU/UG   -0.69   -0.62    3.16    3.87    0.05   -5.38
  17 UG/GU   -1.13    9.00   12.68   -1.60    9.15   12.56
  18 GU/UG   -2.66    2.33    7.98   -3.11   -1.49    5.97
  19 UA/UU    1.44    7.36    8.41    1.48    7.36    8.39
  20 Ag/gU    ---     ---     ---     ---     ---     ---     ---
  21 gG/Gg   -1.88   -0.50    6.72   -3.52   -0.95    6.73
  22 GG/GG    2.93   -8.32    9.69    0.64  -11.88    7.20
  23 GU/UG   -0.93   -5.19    0.60   -0.36   -5.24    0.05

(this structure has x on for a step without a continuous backbone- from the DSSR output; 3dna just leaves them blank)


    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 ga/TC   -2.77    8.59    0.69   -3.28    8.62    0.28
   2 ac/GT   -2.49    8.71    1.70   -4.62    8.57    2.22
   3 ca/TG   -3.29    8.69    1.01   -7.71    7.93    3.84
   4 ac/GT   -3.02    9.01    1.11   -8.02    8.96    1.50
   5 cc/GG   -1.93    8.22    2.51   -5.41    7.78    3.66     A
   6 cu/AG   -2.26    8.95    1.99   -6.31    9.06    1.61     A
   7 ug/CA   -2.51    8.67    1.19   -4.74    8.70    1.07
   8 ga/uC   -2.43    8.87    1.41   -6.30    7.97    4.14
   9 au/Au   -2.90    8.63    0.53   -5.39    8.55    1.15
  10 uu/AA   -2.76    8.87    1.25   -8.18    8.07    3.92
  11 uc/GA   -2.38    8.52    1.92   -5.00    8.39    2.38


9 percent A..?



3DNA has been incredible to use so far, very multi-dimensional and comprehensive.
Thank you.

28
Thanks, Mauricio, for chiming in and for your nice words about my early publications.

Quote from: Puru
I was wondering if there is a script , another way to classify the structures that I have compiled by A, B, AB, TA- type( which is done and seen on the forum)?

Could you please clarify your question, preferably with a concrete example?

Xiang-Jun
29
Programs / Re: blocview
« Last post by xiangjun on June 20, 2018, 01:21:05 pm »
Hi Mauricio,

Nice to see you again on the 3DNA Forum!

Quote
I would also like to change the radius of the sticks representing the sugar-phosphate backbone bonds.

The default radius of the sticks is set via the r3d_atom -r=0.16 option in the blocview script. See the excerpt below:

Code: Ruby
  1.         # color nucleic-acid base/sugar by residue type
  2.         Utils.run_cmd("#{$x3dna}r3d_atom -ncz -r=0.16 tb.pdb #{$temp_r3d} #{$msg}")
  3.         Utils.append_r3dfile(opts[:r3dfile], $temp_r3d)

So you may change the radius 0.16 to your preferred value.


Alternatively (and preferably), you may want to give DSSR a try. DSSR has integrated blocview as a command-line option, and employes PyMOL for rendering. See the DSSR User Manual for more details.

HTH,

Xiang-Jun

 
30
Programs / blocview
« Last post by mauricio esguerra on June 20, 2018, 08:44:54 am »
Hi Xiang-Jun,

In using blocview I know that the radius of the backbone tube which traces the phosphate atoms can be changed in the last line of the $X3DNA/config/col_chain.dat file.

Nonetheless I would also like to change the radius of the sticks representing the sugar-phosphate backbone bonds.
I can do this manually by altering the resulting .r3d files, say, if one of these bond specifications as a cylinder in raster3D is:

Code: [Select]
3
  -10.965  -18.757   -1.704    0.160   -9.568  -18.592   -1.909    0.160    1.000    1.000    0.000

I can change the 0.160 value in the fourth and eight fields to whichever radius I want.
I was wondering if there's a file where this parameter can be changed in an easier way.

Thanks,

Mauricio

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.