Topics

1

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

2

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

3

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.