Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL

Author Topic: DSSR issue --json and --analyze  (Read 704 times)

Offline jyesselm

  • non-commercial
  • Verified Member
  • *
  • Posts: 5
    • View Profile
DSSR issue --json and --analyze
« on: April 19, 2020, 11:20:27 pm »
Hi Xiang-Jun,

I must again commend you on your amazing software. Not only is it quite useful but you are incredibly responsive to issues.

I have downloaded your new version of DSSR and love the json support. I noticed though that if I use both --json and --analyze it will suppress the json output. It would be amazing if you can add in the --analyze info into the json.

x3dna-dssr -i=S_000001.pdb --json --analyze

Best,
Joe

Offline xiangjun

  • Administrator
  • Verified Member
  • *****
  • Posts: 1528
    • View Profile
    • 3DNA homepage
Re: DSSR issue --json and --analyze
« Reply #1 on: April 19, 2020, 11:49:49 pm »
Hi Joe,

Thanks for your kinds words about DSSR ... not all people are appreciative of what I would call a "solid software product". To some "experts", DSSR is a project all done, nothing more worthing to be added.

I added the --analyze mainly to obsolete the analyze program of 3DNA, which is still maintained but no more new features. As documented in the DSSR manual, an alternative form of this option is --3dna-v2. So when the --analyze is enabled, DSSR generates a text output similar to the original 3DNA analyze program. In other words, the DSSR --analyze is working as initially designed.

As always, I'm open to suggestions from users like you. You're the first person (as far as I can recall) who has actually asked a question on this --analyze option in DSSR. What parameters from the --analyze option are missing in DSSR with --json for your project?

Best regards,

Xiang-Jun


« Last Edit: April 20, 2020, 09:36:29 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

Offline jyesselm

  • non-commercial
  • Verified Member
  • *
  • Posts: 5
    • View Profile
Re: DSSR issue --json and --analyze
« Reply #2 on: April 20, 2020, 11:23:42 am »
Hi Xiang-Jun,

Thank you for your prompt response. I understand your point. This is just an ease of use feature. I can get everything I need by calling DSSR twice and parsing the old x3dna data via text. If you have time though I would love you to include the information from dssr-pairFrames.txt in your json dictionary under 'refFrames' that would be amazing. I am after both the origin and reference frame matrix.

I think you could accomplish this with the below format.

1 G1             C11            G-C WC           19-XIX    cWW  cW-W
        3.614304         2.453535        -9.939577      # origin
       -0.564447        -0.824117        -0.047238      # x-axis
        0.817888        -0.566084         0.102998      # y-axis
       -0.111623         0.019502         0.993559      # z-axis

would be

{'index' : 1, 'nt1' : 'G1', 'nt2': 'C11', 'bp' : 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W',
'origin':  '3.614304         2.453535        -9.939577', 'x-axis': '-0.564447        -0.824117        -0.047238', 'y-axis' :  ' 0.817888        -0.566084         0.102998', 'z-axis' : ' -0.111623         0.019502         0.993559'}

Best,
Joe

Offline xiangjun

  • Administrator
  • Verified Member
  • *****
  • Posts: 1528
    • View Profile
    • 3DNA homepage
Re: DSSR issue --json and --analyze
« Reply #3 on: April 20, 2020, 11:29:04 am »
Hi Joe,

Did you know that the base-pair reference frame info is already available in the JSON output? For example,

Code: Bash
  1. # Note the --more option
  2. x3dna-dssr -i=355d.pdb --json --more | jq '.pairs[0].frame'
  3. # You'll get the following output:
  4. {
  5.   "rmsd": null,
  6.   "origin": [
  7.     17.127,
  8.     25.962,
  9.     25.878
  10.   ],
  11.   "x_axis": [
  12.     -0.987,
  13.     0.154,
  14.     0.038
  15.   ],
  16.   "y_axis": [
  17.     0.121,
  18.     0.886,
  19.     -0.447
  20.   ],
  21.   "z_axis": [
  22.     -0.103,
  23.     -0.436,
  24.     -0.894
  25.   ],
  26.   "quaternion": [
  27.     -0.036,
  28.     0.071,
  29.     0.971,
  30.     -0.228
  31.   ]
  32. }

Is that what you want?

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

Offline jyesselm

  • non-commercial
  • Verified Member
  • *
  • Posts: 5
    • View Profile
Re: DSSR issue --json and --analyze
« Reply #4 on: April 20, 2020, 11:32:50 am »
yes! thank you so much I did not realize that. That solves my problem. I didn't see that in the documentation.

Best,
Joe

Offline xiangjun

  • Administrator
  • Verified Member
  • *****
  • Posts: 1528
    • View Profile
    • 3DNA homepage
Re: DSSR issue --json and --analyze
« Reply #5 on: April 20, 2020, 11:39:26 am »
Hi Joe,

Glad to see that helped.

Quote
I didn't see that in the documentation.

As I mentioned in several places already, DSSR has (far) more features than documented. The User Manual is already 108-page long, and I doubt few users read it through, not to mention fully understand/appreciate the details. That's understandable. It is better to claim less but deliver more, rather than the other way around. That's just my way of thinking and performing research, at least.

Best regards,

Xiang-Jun
« Last Edit: April 20, 2020, 01:17:48 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

Offline jyesselm

  • non-commercial
  • Verified Member
  • *
  • Posts: 5
    • View Profile
Re: DSSR issue --json and --analyze
« Reply #6 on: April 20, 2020, 12:45:31 pm »
Yes understood. Thanks again for your help.

 

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.