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Questions and answers => RNA structures (DSSR) => Topic started by: jimamoto on March 08, 2019, 10:14:38 pm

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Title: Using dssr to analyze PDB containing multiple frames
Post by: jimamoto on March 08, 2019, 10:14:38 pm
Hello,
I am trying to use dssr to analyze a pdf file containing multiple frames.  Unfortunately, when I use dssr whether I use --nmr or --json it only gives me information on a single frame.  I have tried adding model to the name of the output file, but it does not produce torsions for each one.  I am new at using dssr and I figure I am making a simple mistake. 
Below are two of the ways I have tried to call dssr.
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr -json -o=Lin2_Lay8_NoWat_Frame_1-100-all.json
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr  -o=Lin2_Lay8_NoWat_Frame_1-100-model.out

Thank you for your time and help.

Jason Imamoto
Title: Re: Using dssr to analyze PDB containing multiple frames
Post by: xiangjun on March 08, 2019, 10:16:30 pm
Please provide an example file, command options, and the output file, to show the problem concretely.

Thanks,

Xiang-Jun
Title: Re: Using dssr to analyze PDB containing multiple frames
Post by: jimamoto on March 08, 2019, 10:31:55 pm
Attached is a few output files that I received when I ran the command.

The exact command entered
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr  -o=Lin2_Lay8_NoWat_Frame_1-100-model.out
The output contains only 1 model out of the 100 that were in the pdb.

Also I forgot to mention I am running  v1.7.7-2018apr20 of dssr.

Thank you.
Jason Imamoto
Title: Re: Using dssr to analyze PDB containing multiple frames
Post by: xiangjun on March 08, 2019, 10:45:24 pm
OK. Now I understand your point.

For the analysis of an NMR ensemble or MD trajectories, the --json option is the approach to go. Using 2n2d as an example, as given from DSSR -h or --help, you could:

Code: Bash
  1. x3dna-dssr -i=2n2d.pdb --nmr --json -o=2n2d-dssr.json
  2. # the following command extracts parameters related to the first nucleotide of the first model (with index 0)
  3. jq .models[0].parameters.nts[0] 2n2d-dssr.json

See the thread "DSSR: Analyzing NMR structures - overwritten output files (http://forum.x3dna.org/rna-structures/dssr-analyzing-nmr-structures-overwritten-output-files/)". The R script by Markus should be of help.

Best regards,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University