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Messages - Marcel Heinz

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1
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

2
Hi Xiang-Jun,

Thank you so much for the DSSR update. I do apologize for the inconvenience of not having a trajectory, but I was traveling with an unexpectedly unstable internet connection.
Just arrived back and tested your latest DSSR version with my 100k structure trajectory.
Your update has a dramatic speed up in analyzing the trajectory. Great improvement!
 
Quote
Time used: 00:00:35:59

Are you still interested in a 10k structure trajectory?

Best regards,

Marcel

3
Hi Xiang-Jun,

Code: [Select]
do_x3dna -f ../mod.pdb -s ../mod.pdb -o test -hbond
and extract the dihedral information from "BackBoneCHiDihedrals_g.dat"

Could you dig further to see what 3DNA command is being called with the above do_x3dna run? What is the -hbond option? What's the do_x3dna output looks like? Do you only need backbone torsion angles?
1. I honestly don't know which exact 3DNA commands are being called, but I get all structural informations in separate output files. I could refer to the official webpage where you see all the outputs listed below: https://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html
2. The -hbond flag calculates the number of H-bonds per basepair and timeframe. The ASCII ouputfile (h-bond_g.dat) looks like this for three basepairs
Quote
# Time =         1.00000
3
3
2

# Time =         2.00000
3
3
2
3. The ouput files are in ASCII format and column based, for the dihedrals, they do look like this
Quote
#Strand I                                                    Strand II
#alpha    beta   gamma   delta  epsilon   zeta    chi   |||  alpha    beta   gamma   delta  epsilon   zeta    chi

# Time =         1.00000
---   ---   54.5   85.7   -156.4   -76.3  -152.6  -88.4   -175.1   69.5   86.2   ---   ---  -114.5
-71.8   162.2   59.7   82.7   -164.5   -64.9  -163.0  -86.6   -175.1   54.5   72.1   178.6   -70.4  -136.6
-76.8   -178.7   53.6   74.4   -160.4   -64.9  -149.9  -71.7   169.9   60.6   78.4   -157.3   -57.9  -140.9
-70.2   172.9   68.1   66.9   -159.9   -59.8  -150.7  -73.8   171.8   63.5   69.0   -157.2   -61.2  -145.9
-73.0   178.7   54.8   81.2   -175.2   -59.1  -146.4  -71.9   166.1   76.6   76.4   -154.5   -64.2  -167.3

4. The overall structure parameter are of my general interest. But for now, I'm especially interested in the backbone dihedral angles.



Would it be possible that you provide me a sample MD trajectories file?
The data are unpublished, so if you could provide me a way of sharing it in a non-public way (e.g. email address), I'm able to provide a native trajectory.

Just as a note: I continued the DSSR analysis since yesterday and frame 14762 is currently loaded, so I do agree to the memory issue.

Best,

Marcel

4
Thanks a lot for your very fast reply!

To investigate this issue further, could you elaborate on how you calculated the backbone parameters using do_x3dna? Does do_x3dna call the 'analyze -t' (for torsion angles) option?
I do run do_x3dna on a native RNA (no abasic site) trajectory with

Code: [Select]
do_x3dna -f ../mod.pdb -s ../mod.pdb -o test -hbond
and extract the dihedral information from "BackBoneCHiDihedrals_g.dat"

To investigate this further, I started the analysis an hour ago and 53,000 frames are currently analyzed with do_x3dna.

In contrast, I run DSSR now with the latest version (downloaded today) on the same pdb-trajectory with

Code: [Select]
x3dna-dssr -i=mod.pdb -o=output.json --more --json --nmr
and currently it runs for frame 2,100.

Based on my impression, DSSR and do_x3dna are approx. similar in analyzing the first ~1000 structures and DSSR gets slower and slower with every following structure.
As a workaround, I could cut my trajectory into 1000 structure fragments and analyze them independently, but I think the performance issue is important especially for the MD community to work with DSSR.


For your second question, what version of DSSR were you using? This bug should have been fixed in the later releases of DSSR, as shown below:

Code: [Select]
Processing file 'frame1630.pdb'
  X.U.7               0.121
  X.U.42              0.143
    total number of nucleotides: 44
    total number of base pairs: 20
    total number of helices: 1
    total number of stems: 3
    total number of internal loops: 2

Also, note that you do not need to specify the --abasic option anymore. This feature is taken into consideration by default in recent releases of DSSR.

Thank you very much. Indeed, I was using an older version of DSSR and it seems to work with your latest version (frame 1630 does not crash). And thank you for the hint with the default --abasic command. I just followed the manual to this: http://x3dna.org/articles/handling-of-abasic-sites-in-dssr

Best,

Marcel

5
Dear Xiang-Jun,

Thanks a lot for your work and support here.
I currently have two issues with DSSR:

1.
Do you have an idea why the backbone parameter for a nucleic acids are so much faster calculated with do_x3dna than with DSSR? Analyzing a trajectory with 100k frames take for a native structure approx. 2 hours with do_x3dna. A native RNA structure with DSSR will take approx. 10 days (10k frames/day). I need to run DSSR, because my system contains an abasic site.

I used this command line:

Quote
x3dna-dssr -i=mod.pdb --nmr --json --abasic -o=mod.json

2.
I also run into problems with DSSR while trying to analyze a MD trajectory (100k structures) of a ~40 NA duplex structure, containing an abasic site. DSSR crashes with an error message at frame 1630 for the abasic site with the error message

Quote
model 1630 [1630 of 100000]
  1630.X.U.7          0.121
  1630.X.U.42         0.143
Uncaught exception 'Assertion failed' raised at [fncs_hbond.c:1762]
aborting...

The frame seems to be ok in the pdb file (s. attachement). Do you have an idea of what might be going wrong?

Best,

Marcel

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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.