Messages

1

RNA structures (DSSR) / Re: Criteria of Identification of hydrogen bonds

« on: June 10, 2016, 02:12:22 pm »

Hi Xiang-Jun,

Thank you very much for your reply. I don't have access to HBPLUS or HBexplore yet, though I've contacted HBPLUS development team for the installation file. If you know an easy way to access to them, just let me know. I'd love to do a further test and comparison.

As you pointed, could you explain type 'o' and '?' a little further? What are the other atoms in "

‘o’ for a donor/acceptor (such as the 2′-hydroxyl oxygen) with any other atom;

" and why there could be a hbond even though "

the donor/acceptor status of any H-bond atom is unknown

". Examples should help.

Thanks,

JJ

2

RNA structures (DSSR) / Re: Criteria of Identification of hydrogen bonds

« on: June 09, 2016, 05:04:45 pm »

Xiang-Jun,

I appreciate your honest reply. Now I may wanna bother you with a test case I just did. The hbond result from dssr is

Code: [Select]

# H-bonds in '4DII_aptamer_autopsf.pdb' identified by DSSR, Xiang-Jun Lu (xiangjun@x3dna.org)
18
   16   189  #1     p    3.070 N:N N2@D.GUA1 N7@D.GUA6
   21   187  #2     p    2.941 N:O N1@D.GUA1 O6@D.GUA6
   24   481  #3     p    2.781 O:N O6@D.GUA1 N1@D.GUA15
   26   476  #4     p    2.816 N:N N7@D.GUA1 N2@D.GUA15
   49   449  #5     p    2.789 N:N N2@D.GUA2 N7@D.GUA14
   54   447  #6     p    2.970 N:O N1@D.GUA2 O6@D.GUA14
   57   151  #7     p    2.640 O:N O6@D.GUA2 N1@D.GUA5
   59   146  #8     p    2.737 N:N N7@D.GUA2 N2@D.GUA5
  154   347  #9     p    3.001 O:N O6@D.GUA5 N1@D.GUA11
  156   342  #10    p    2.987 N:N N7@D.GUA5 N2@D.GUA11
  179   319  #11    p    2.907 N:N N2@D.GUA6 N7@D.GUA10
  184   317  #12    p    2.849 N:O N1@D.GUA6 O6@D.GUA10
  244   291  #13    p    3.965 N:O N2@D.GUA8 O3'@D.THY9
  244   302  #14    p    3.073 N:O N2@D.GUA8 OP2@D.GUA10
  309   486  #15    p    3.002 N:N N2@D.GUA10 N7@D.GUA15
  314   484  #16    p    2.894 N:O N1@D.GUA10 O6@D.GUA15
  350   444  #17    p    2.574 O:N O6@D.GUA11 N1@D.GUA14
  352   439  #18    p    2.762 N:N N7@D.GUA11 N2@D.GUA14

However, to my understanding, this ssDNA should have 2 G-tetrads with 16 hbonds but dssr returned 18. I suspect this was because it counted the hbonds involved in phosphate. However, another test pdb shows more complicated results. Particularly, the same acceptor atoms involve in p-type hbond and x-type simultaneously. I was wondering if you could take a look at those attached pdbs to check whether the results from dssr are reasonable.

Thanks again.

JJ

3

RNA structures (DSSR) / Re: Criteria of Identification of hydrogen bonds

« on: June 09, 2016, 03:35:56 pm »

Xiang-Jun,

It's good to hear you'd like to release some source code. To answer your question, 1) it appears to me 3DNA/DSSR has been optimized for identification of h-bond according to your description in your paper, which leads me to come here with above questions I asked. 2) I'm working on a project specifically on folding/unfolding nucleic acids, where the hbond statistics can help quantify the possible interesting structures (e.g. G-quadruplex). In such case, HBPLUS or HBexplore might not be well tuned as your program though I haven't tested with them. What do you think according to your experience? Do you think your algorithm indeed has particular merits on nucleic acids in comparisons with others that simply consider the distance between donor and receptor and angles?

As you could probably tell, it should make me clearer and more comfortable to pick DSSR instead of others if I could understand what specific optimization of your algorithm is.

JJ   

 

4

RNA structures (DSSR) / Re: Criteria of Identification of hydrogen bonds

« on: June 09, 2016, 01:27:00 pm »

Xiang-Jun,

Thanks for your fast reply. What does "mutual best match" specify? Does it include a consideration of the angle? How does the algorithm avoid the spurious hydrogen bonds?

 JJ

5

RNA structures (DSSR) / Criteria of Identification of hydrogen bonds

« on: June 09, 2016, 12:13:56 pm »

Hi Xiang-Jun,

Could you elaborate your heuristic criteria of the identification of hydrogen bonds  in DSSR? I understand it is geometric based. But I couldn't find the details except for the distance cutoff in the DSSR paper in NAR.
Thanks!

JJ

6

RNA structures (DSSR) / Re: No nucleotides identified from VMD selected ssDNA structure

« on: November 24, 2015, 02:49:45 pm »

Hi Xiang-Jun,

Thank you for your fast reply. I saw similar thing you saw in VMD. I wonder how the visualization softwares (looks like pyMol you were using) and dssr determine the connections between atoms. I checked the atom orders  in both pdbs I attached. They look the same.

JJ

7

RNA structures (DSSR) / No nucleotides identified from VMD selected ssDNA structure

« on: November 24, 2015, 02:13:16 pm »

Dear Xiang-Jun,

Yep. Let's keep informed.

I experienced some issues when using DSSR today. The ssDNA I extracted from the a MD trajectory of the protein-DNA complex (using VMD selection cmd-select "nucleic") seems not be able to identified as a DNA/RNA chain by DSSR. I will attach the pdb I used (Frame1.pdb) and the relevant psf and pdb in expect in this post. Can you take a look at it when you had a chance?

Thanks!

JJ

8

RNA structures (DSSR) / Re: different get-hbond output

« on: November 21, 2015, 11:33:41 pm »

Xiang-Jun,

Thanks again for your detailed and enlightening reply!

I do agree the hydrogen pairing output from dssr is meaningful, especially when studying the dynamics of nucleic acids and relevant network.

Currently I still take the strategy to convert the dcd into individual pdbs and analysis them one by one. I'd love to share my feedback about my experience about it in case you liked to know. The processing speed is OK right now but it might be better if they can be processed in parallel.

JJ

9

RNA structures (DSSR) / Re: different get-hbond output

« on: November 21, 2015, 10:46:37 pm »

Hi Xiang-Jun,

Thank you very much for your prompt and helpful reply.

You pointed I didn't need to specify --po4 for getting h-bonds. However, in the manual, it has a description on this option:

Code: [Select]

The phosphate group in RNA is negatively charged, with four oxygen atoms that could
serve as H-bond acceptors or be in coordination with metals. T
Does it mean in the get-hbonds function includes --po4 by default?

A new question is about the order of donor/acceptor pair. I notice

Code: [Select]

It is ‘p’ for a donor-acceptor atom pair; ‘o’ for a donor/acceptor. Thus I'm thinking whether the residue number of first residue(atom) must be smaller than the second one.

Thank you for your help and work again.

JJ

10

RNA structures (DSSR) / different get-hbond output

« on: November 21, 2015, 04:26:08 pm »

Hi Xiang-Jun,

I'm trying to use x3dnr-dssr to find pairs of hydrogen bonds in a MD trajectory. I converted the dcd trajectory to a bunch of pdbs first and employ dssr to analyze each frame individually using the command line like:

Code: [Select]

/Applications/x3dna/x3dna-dssr-v1.4.2-2015oct19/x3dna-dssr --po4 --idstr=short -i=Frames1.pdb --get-hbonds -o=hbonds.txt > dssr.log 

Then following content about the intermediate processing status was displayed in the terminal.

Code: [Select]

Processing file 'Frames1.pdb'
N1.D.THY.3 0.122
N1.D.THY.7 0.121
N1.D.THY.9 0.120
N1.D.THY.12 0.122
N1.D.THY.13 0.133

Time used: 00:00:00:00
I realize the output file hbonds.txt has different content, which is

Code: [Select]

# H-bonds in 'Frames1.pdb' identified by DSSR, Xiang-Jun Lu (xiangjun@x3dna.org)
1
  206   244  #1     p    3.002 O:N O5'@THY7 N2@GUA8

I wonder what the content displayed is during the processing and how to turn off displaying the processing status information since I'll have two many frames to process on the queque. I found you mentioned quiet mode in following thread: http://forum.x3dna.org/general-discussions/option-not-to-display-calculation-status-to-screen/msg352/#msg352.

I found dssr can understand the flag -quiet instead of -q. However, "Processing file 'Frames1.pdb'" still occurred even with that flag. And I find the intermediate status does not occur every time for different files, which confused me more.

I hope my description is clear. Could you help me understand 1. the differences in the processing output and file output. 2. How to turn off the displaying in the terminal. 3. Is there any better way to use dssr to analysis a trajectory. 4. Is it possible to have some flag like --get-multiplets, --get-stacks?

The pdb file will be attached in this thread.