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11
Dear Xiang-Jun,

I have been having trouble rebuilding the base reference frames from the middle frame and base pair parameters outputted by x3DNA/DSSR.

Middle Frame: [[0.825, 0.565, 0.001], [-0.565, 0.824, -0.032], [-0.018, 0.026, 1.0]]
Base Pair Parameters: [-0.176, -0.054, 0.306, -0.548, -9.232, -3.527]

I am implementing the method from the x3DNA user manual (attached below). It seems that one of the frames I am calculating (labeled F2) has its y and z axes reflected.

Reference Frames calculated by me:
F1c: [[ 0.838,  0.54   ,  0.082], [-0.539,  0.841, -0.034], [-0.087, -0.016,  0.996]]
*F2c: [[ 0.806,  0.586, -0.0802], [-0.59,  0.807, -0.025], [ 0.051 ,  0.067,  0.996]]

*y and z axes are reflected

Reference Frames outputted by DSSR:
F1: [[0.838, 0.54, 0.082], [-0.539, 0.841, -0.034], [-0.087, -0.016, 0.996]]
F2: [[0.806, 0.587, -0.081], [0.59, -0.807, 0.024], [-0.051, -0.067, -0.996]]

I can just multiply the frame by this matrix: [[ 1,  0,  0], [ 0, -1,  0], [ 0,  0, -1]], but I was wondering what might be wrong with my implementation.

I have attached the formulas I am using, as well as the pdb I am analyzing and DSSR json file output. Let me know if I should attach anything else that may be helpful.

Edit: The bases I am analyzing in the pdb file are the modified 8OG-C pair (Base numbers 2 and 5).

Thank you for your time,
Nil

12
RNA structures (DSSR) / Re: Seeking help with DSSR (Base Pair and Stacking)
« Last post by xiangjun on October 09, 2018, 01:16:15 pm »
Quote
Can you please help me to compare the 'adjacent and non-adjacent stacking' of MC-Annotate output with something in DSSR output?

In DSSR output, the fact that stacked bases are covalently connected via a phosphodiester bond is noted by the keyword "connected". For example, for 1ehz (a tRNA), you'd see the following in DSSR output. For entry #68, the stacking between G51 and U52 is marked by connected, while the other two entries do not.

 # x3dna-dssr -i=1ehz.pdb --non-pair
List of 93 non-pairing interactions
......
36 A.A21    A.C48    stacking: 5.9(2.9)--mm(<>,outward) interBase-angle=5 min_baseDist=3.28
68 A.G51    A.U52    stacking: 6.8(4.0)--pm(>>,forward) interBase-angle=6 connected min_baseDist=3.22
71 A.G53    A.A62    stacking: 4.2(2.0)--mm(<>,outward) interBase-angle=8 min_baseDist=3.15


It is up to you to compare the DSSR output with that from MC-Annotate. You're welcome to post your finding here for the benefit of other viewers of the thread.

HTH,

Xiang-Jun
13
RNA structures (DSSR) / Re: Seeking help with DSSR (Base Pair and Stacking)
« Last post by mahfuz on October 09, 2018, 12:16:56 pm »
Thank you for your quick response. I was just trying to compare the outputs from MC-Annotate, RNA-View and DSSR. There is something 'adjacent' and 'non-adjacent' stackings showing in MC-Annotate. I mistakenly wrote 'canonical and non-canonical' for these terms. I'm extremely sorry for my mistake.

Can you please help me to compare the 'adjacent and non-adjacent stacking' of MC-Annotate output with something in DSSR output?

Thanks
14
RNA structures (DSSR) / Re: Seeking help with DSSR (Base Pair and Stacking)
« Last post by xiangjun on October 05, 2018, 10:11:08 pm »
Hi Mahfuz,

Quote
The canonical and non-canonical stackings are not clear to me.

Where did you get the concept of canonical vs non-canonical stackings from? What do you mean specifically? It is not a term used in DSSR.

In DSSR, pairwise stacking interactions are available via the --non-pair option, as documented in the -h option and the manual. Stacking interaction is detected and quantified by the overlap area of bases.

Quote
I'm also trying to get the direction of the stackings (upword/downword/inward/outward).

Check section "3.8 The --non-pair option" of the DSSR manual:

Quote
As in 3DNA [8], base-stacking is quantified as the area (in Å2) of the overlapped polygon defined by the two bases of the interacting nts, where the base atoms are projected onto the mean base plane9. In the output file, values in parentheses measure the overlap of base ring atoms only, and those outside parentheses include exocyclic atoms on the ring. Base-stacking interactions are classified into one of the following four categories: pm(>>,forward), mp(<<,backward), mm(<>,outward), and pp(><,inward). Here p and m represent the plus and minus faces of the base ring, as defined by the direction of the z-axis of the standard base reference frame. The symbols (>>, <<, <>, and ><) follow Major et al, except pm(>>) is called forward instead of upward, and mp(<<) backward instead of downward [32]. Moreover, the inter-base angle is reported; closer to zero means the two bases are nearly parallel.

Basically, each base has two faces (just as a coin). See Fig. 1 of the DSSR paper, attached below (also the 2003 3DNA paper). Each z-axis has a minus--->plus directionality, and there are 2x2=4 possible combinations of two bases in stack, as noted above.

"summary of methods to identify RNA structural components" title="summary of methods to identify RNA structural components"

HTH,

Xiang-Jun
15
RNA structures (DSSR) / Seeking help with DSSR (Base Pair and Stacking)
« Last post by mahfuz on October 05, 2018, 05:49:11 pm »
Hi Dr. Xiang-Jun Lu,

I'm working on your annotation tool DSSR and trying to get the base-pair and stacking information from DSSR annotation. The base-pair part is clear enough but I'm facing problem for finding the stackings. The canonical and non-canonical stackings are not clear to me. I'm also trying to get the direction of the stackings (upword/downword/inward/outward).

Thanks

Mahfuz
16
RNA structures (DSSR) / Re: DSSR Download and Installation
« Last post by xiangjun on September 26, 2018, 06:48:51 pm »
Hi,

Please check the following two things:

  • The .dms extension (thus x3dna-dssr.dms instead of the intended x3dna-dssr) is added by Safari on macOS. Using the Google Chrome browser won't have the problem. To avoid confusion, you could simply remove the extra extension by: mv x3dna-dssr.dms x3dna-dssr
  • Change the access permissions of the downloaded x3dna-dssr file, by using the chmod u+x command option to make it executable. Then DSSR should work -- check it out: x3dna-dssr -h

I've updated the DSSR User Manual with a note on the extra .dms on macOS. Please read it and let me know if anything is still unclear.

HTH,

Xiang-Jun
17
RNA structures (DSSR) / DSSR Download and Installation
« Last post by se3DNAcct on September 26, 2018, 04:17:18 pm »
Hello,

When I download the DSSR executable for MacOS, I only get the following text file whose contents are unintelligible.  How can I get the correct download in order to install DSSR?  Please advise; your help is much appreciated!

Thank you very much.


Note added by Xiang-Jun: the attached DSSR program for macOS was removed on 2019-09-27.
18
RNA structures (DSSR) / Re: Analysis crashes: MD trajectory of abasic site in RNA
« Last post by xiangjun on September 06, 2018, 01:48:00 pm »
Quote
I've send you an email with a link to download the trajectory to xiangjun@x3dna.org

Got it -- thanks!

Quote
Just as a short note: I have to look deeper into it, but the output.json file has a size of 6.8G, while the do_x3dna files have combined only 992M.  Is the --json flag mandatory for trajectories or do the 'normal' output-files also contain frame informations?

The much larger output file from DSSR than that from do_x3dna is expected. DSSR produces far more RNA structural parameters than other tools I'm aware of. So the JSON output contains far more than you need (torsion angles) right now. However, other DSSR-derived features are of potential use in other projects, as DSSR is used more widely in the MD field.

The --json flag is not mandatory for trajectories, but only the JSON output contains a complete compilation of DSSR parameters. Otherwise, the torsion angles are not listed in 'normal' output file. Check the DSSR manual for more info.

In practice, you could use a tool like jq to filter the stream of JSON data produced by DSSR. This could produce a smaller output file than that from do_x3dna.

Best regards,

Xiang-Jun




19
Bug reports / Re: 5-hydroxy methyl cytosine
« Last post by shuxiang on September 06, 2018, 01:22:27 pm »
I have modified web 3DNA to deal with modified cytosine like 5HM. :)
20
RNA structures (DSSR) / Re: Analysis crashes: MD trajectory of abasic site in RNA
« Last post by Marcel Heinz on September 06, 2018, 11:42:33 am »
Indeed, it is much faster than do_x3dna. Great work!

I've send you an email with a link to download the trajectory to xiangjun@x3dna.org

Just as a short note: I have to look deeper into it, but the output.json file has a size of 6.8G, while the do_x3dna files have combined only 992M.  Is the --json flag mandatory for trajectories or do the 'normal' output-files also contain frame informations?

Best,

Marcel
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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.