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Messages - meier74

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1
Dear all,

here is a working example how to read the JSON output from x3dna-dssr in an R script and produce a backbone torsion angle plot from the NMR ensemble PDBID 2M4P (a DNA G-quadruplex). I have attached a compressed tar archive (for those unfamiliar with this format, use 7-Zip, http://www.7-zip.org to extract). Please refer to INSTRUCTIONS.txt on how to use it. The script is made available under the MIT license.

Best regards,
Markus

2
Hi Xiang-Jun,

many thanks again for introducing the "nt_resnum" field into the "nts" record of the JSON output! I have attached version 3 of the example script that takes advantage of the new feature. I will also post a fully working example that produces a plot of the backbone torsion angles soon, as promised.

Best regards,
Markus

3
Hi Xiang-Jun,

A new "nt_resi" field with the residue number as below would help:

  "nts": [
    {
      "index": 1,
      "index_chain": 1,
      "chain_name": "A",
      "nt_resi": 2,
      "nt_name": "DG",
      "nt_code": "G",
      "nt_id": "A.DG2",
...
  }]

This would allow to extract all the essential data with the same block of code. I did not know about the --idstr option which changes the nt_id field to ".A.DG.2.". This one makes pattern matching a safe bet and works as well, but needs a little extra code. So, if you think it is not worth the effort to add an "nt_resi" field, do not worry about it.

Best regards,
Markus



4
Hi Xiang-Jun,

you are very welcome. I found some problem with the script. Since x3dna-dssr does not record the nucleotide/residue numbers in the JSON data structure, I have used the index field in lieu of the residue numbers. Unfortunately, this gives incorrect results, if the nucleotide numbers do not start from 1 or are not consecutive. I have attached a revised version of the script that extracts the residue number from the nt_id field using pattern matching. However, it might not work in all cases. The best way would be to modify x3dna-dssr so that it also outputs the residue number in the nts record.

Best regards,
Markus

5
Hi everyone,

I have attached a short R script that reads the JSON output from x3dna-dssr and puts into a tidy table. Using dplyr's filter() function, you can select the parameters for the nucleotides you are interested in (filter for chain ID, nucleotide number, nucleotide name etc...), similar to a Pymol selection. Pretty cool!
The script requires dplyr and tidyjson libraries which can be obtained from CRAN.

I hope it will help someone else.

Best regards,
Markus

--
Markus Meier, Ph.D.
Research Associate
University of Manitoba
Department of Chemistry
144 Dysart Road
Winnipeg, MB, R3T 2N2, Canada
E-mail: markus.meier@umanitoba.ca

6
Hi  Xiang-Jun,

long time no see :-)

Thanks for the suggestion, I will give it a try. I am current using R to make some figures, it has libraries for read JSON.

Best regards,
Markus

--
Markus Meier, Ph.D.
Research Associate
University of Manitoba
Department of Chemistry
144 Dysart Road
Winnipeg, MB, R3T 2N2, Canada
E-mail: markus.meier@umanitoba.ca

7
Dear all,

I am trying to analyze an NMR ensemble with 10 models using x3dna-dssr with the --nmr option. I am interested in the backbone torsion angles. Unfortunately the file dssr-torsions.txt gets overwritten as the program proceeds from model to model in the PDB file. After the run finishes, the file only contains the data for the last model (#10). Is it possible to configure the program in such a way that it records the data for all models?

I am using DSSR v1.6.5-2017jan22 on Gentoo Linux (64 bit)

Thank you for your help!
Markus

--
Markus Meier, Ph.D.
Research Associate
University of Manitoba
Department of Chemistry
144 Dysart Road
Winnipeg, MB, R3T 2N2, Canada
E-mail: markus.meier@umanitoba.ca

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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.