Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Groove width distance in DSSR  (Read 2316 times)

Offline lvelve0901

  • regular
  • *
  • Posts: 52
    • View Profile
Groove width distance in DSSR
« on: January 25, 2017, 04:58:23 pm »
Hi, xiangjun,

Did DSSR output json files have minor groove width information?

If so, could you kindly tell me where is it stored in the json file?

Best,
Honglue

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1220
    • View Profile
    • 3DNA homepage
Re: Groove width distance in DSSR
« Reply #1 on: January 25, 2017, 06:16:10 pm »
Hi Honglue,

The groove dimensions as in the 3DNA/analyze program are currently not calculated in DSSR. So no minor-groove width info in the JSON output, as of DSSR v1.6.5-2017jan22.

It's not hard to add the groove info in the DSSR JSON output. Do you have any preference as to how to present it in JSON?

From 3DNA/analyze, an example output for 355d is as below:

Code: [Select]
                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 CG/CG       ---       ---       ---       ---
   2 GC/GC       ---       ---       ---       ---
   3 CG/CG      14.3       ---      18.2       ---
   4 GA/TC      12.0      11.9      17.3      17.3
   5 AA/TT       9.7       9.6      19.1      19.0
   6 AT/AT       9.1       9.1      16.4      16.0
   7 TT/AA       9.1       9.1      17.8      17.7
   8 TC/GA       9.6       9.6      18.6      18.6
   9 CG/CG      10.4       ---      19.0       ---
  10 GC/GC       ---       ---       ---       ---
  11 CG/CG       ---       ---       ---       ---

The whole section could be listed as an array of strings. Or each of the four columns can be indexed separately.

What's your thought?

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

Offline lvelve0901

  • regular
  • *
  • Posts: 52
    • View Profile
Re: Groove width distance in DSSR
« Reply #2 on: January 25, 2017, 07:13:54 pm »
Hi, xiangjun,

Thank you so much!

Since minor groove width are dinucleotide step in 3DNA, how about we incorporate them into the 'pairs' in the 'helices' where the step and helical parameters stored?

What do you think?

Best,
Honglue

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1220
    • View Profile
    • 3DNA homepage
Re: Groove width distance in DSSR
« Reply #3 on: January 25, 2017, 08:18:53 pm »
That makes sense. I'll implement this feature by next week (I'm facing a deadline for a ms submission).

I'll keep you informed once a preliminary version is available for you check. Stay tuned.

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

Offline lvelve0901

  • regular
  • *
  • Posts: 52
    • View Profile
Re: Groove width distance in DSSR
« Reply #4 on: January 30, 2017, 03:12:45 pm »
Hi, Xiangjun,

Any update about incorporate groove width in json file?

Here is the an example of the structure I want to calculate and its old output json file using "x3dna-dssr -i=A2dna.pdb -o=A2dna.json --json --more". Hope this will be helpful.

Thank you again for your time.

Best,
Honglue


Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1220
    • View Profile
    • 3DNA homepage
Re: Groove width distance in DSSR
« Reply #5 on: January 30, 2017, 03:24:29 pm »
Hi Honglue,

Thanks for sending me the two files. I did not forget your request, and I am hoping to get it done in a couple of days...

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

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1220
    • View Profile
    • 3DNA homepage
Re: Groove width distance in DSSR
« Reply #6 on: February 03, 2017, 11:52:38 am »
Hi Honglue,

Just to let you know that I've been working on the feature (groove info to DSSR) you requested. While at it, I'm considering to include other related features from the 3DNA analyze program to DSSR, presumably only via the JSON output.

In addition to groove widths, are there other 3DNA features you'd like to see in DSSR JSON output?

Best regards,

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

Offline lvelve0901

  • regular
  • *
  • Posts: 52
    • View Profile
Re: Groove width distance in DSSR
« Reply #7 on: February 03, 2017, 12:13:21 pm »
Hi, xiangjun,

I just want to let you know I really appreciate your help!

For other parameters, I need to think about it and get it back to you. Could you kindly remind me any parameter not included in DSSR but in 3DNA? Did the DSSR manual have something about these "missing" parameters?

I will probably response to you either Saturday or Sunday.

Best,
Honglue

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1220
    • View Profile
    • 3DNA homepage
Re: Groove width distance in DSSR
« Reply #8 on: February 03, 2017, 01:03:55 pm »
Hi Honglue,

I always value users' feedback, like yours.

Have a look of the output from the following command, and check file "355d.out":

Code: [Select]
find_pair 355d.pdb | analyze --abi
I'd add the A/B-index, maybe Zp as well... You'll be able to have access to a test version by early next week (no later than Tuesday, I hope).

Have a good weekend.

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

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1220
    • View Profile
    • 3DNA homepage
Re: Groove width distance in DSSR
« Reply #9 on: February 08, 2017, 10:16:42 am »
Hi Honglue,

I've finally added groove widths into DSSR JSON output, per your request. Now with --more, you will see the groove_widths key in helices/stems output. The corresponding value is an array with 4 numbers: [minor_groove_width, major_groove_width, minor_groove_width_refined, major_groove_width_refined], as they appear in the 3DNA analyze output. For example, "groove_widths":[12.023,11.942,17.338,17.281] for the 4th dinucleotide step in 355d.

As mentioned in my previous responses, some additional features from the 3DNA analyze program have been implemented into DSSR. They will be revealed later.

Please have try and report back how it goes. Note I've not updated the release version on the download page yet. However, the download files have been updated.

Best regards,

Xiang-Jun
« Last Edit: February 08, 2017, 10:19:45 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

  • regular
  • *
  • Posts: 52
    • View Profile
Re: Groove width distance in DSSR
« Reply #10 on: February 08, 2017, 12:16:12 pm »
Hi, xiangjun,

Yes, it works very well! Thank you so much.

I am assuming you are also adding more details to the json output files, right? Is it also ok to add the helix-form (A, B, Z) in the stems and helical sections in the json file?

Best,
Honglue

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1220
    • View Profile
    • 3DNA homepage
Re: Groove width distance in DSSR
« Reply #11 on: February 08, 2017, 12:23:15 pm »
Hi Honglue,

The info is already there, as shown below for 355d.

Code: [Select]
x3dna-dssr -i=355d.pdb --json | jq .stems
You will see the following at the top:

Code: [Select]
[
  {
    "index": 1,
    "helix_index": 1,
    "strand1": "CGCGAATTCGCG",
    "strand2": "GCGCTTAAGCGC",
    "bp_type": "||||||||||||",
    "helix_form": "BBBBBBBBBBB",
    "num_pairs": 12,
    "pairs": [
      {
        "index": 1,
        "nt1": "A.DC1",
        "nt2": "B.DG24",
        "bp": "C-G",
        "name": "WC",
        "Saenger": "19-XIX",
        "LW": "cWW",
        "DSSR": "cW-W"
      },
 ....
]

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

Offline lvelve0901

  • regular
  • *
  • Posts: 52
    • View Profile
Re: Groove width distance in DSSR
« Reply #12 on: February 08, 2017, 12:26:00 pm »
I see.

Could you kindly explain to me the definition of helix-form in DSSR? I think you said it is undocumented right?

Thanks!

Best,
Honglue

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1220
    • View Profile
    • 3DNA homepage
Re: Groove width distance in DSSR
« Reply #13 on: February 08, 2017, 12:42:54 pm »
I've edited my response a bit. See that thread. Basically, it is undocumented yet.

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

Offline lvelve0901

  • regular
  • *
  • Posts: 52
    • View Profile
Re: Groove width distance in DSSR
« Reply #14 on: September 15, 2017, 05:00:36 pm »
Hi Honglue,

I've finally added groove widths into DSSR JSON output, per your request. Now with --more, you will see the groove_widths key in helices/stems output. The corresponding value is an array with 4 numbers: [minor_groove_width, major_groove_width, minor_groove_width_refined, major_groove_width_refined], as they appear in the 3DNA analyze output. For example, "groove_widths":[12.023,11.942,17.338,17.281] for the 4th dinucleotide step in 355d.

As mentioned in my previous responses, some additional features from the 3DNA analyze program have been implemented into DSSR. They will be revealed later.

Please have try and report back how it goes. Note I've not updated the release version on the download page yet. However, the download files have been updated.

Best regards,

Xiang-Jun


Hi Xiangjum,

I just want to kindly make sure that the output groove_widths in the json file should be [minor_groove_width, minor_groove_width_refined, major_groove_width, major_groove_width_refined], not [minor_groove_width, major_groove_width,, minor_groove_width_refined, major_groove_width_refined], right?

Best,
Honglue

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.