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Author Topic: Implement Json  (Read 781 times)

Offline lvelve0901

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Implement Json
« on: March 10, 2018, 09:43:32 pm »
Hi Xiangjun,

Do you plan to implement Json output for SNAP?

Best,
Honglue

Offline xiangjun

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Re: Implement Json
« Reply #1 on: March 10, 2018, 09:44:41 pm »
Yes.
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: Implement Json
« Reply #2 on: March 10, 2018, 09:45:52 pm »
Awesome.

Could you please let me know when you finish it?

Best,
Honglue

Offline xiangjun

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Re: Implement Json
« Reply #3 on: March 10, 2018, 09:52:37 pm »
No timeline, as SNAP is still evolving, and nothing has been published on it yet

Could you tell me what you’re using SNAP for?

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

Offline lvelve0901

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Re: Implement Json
« Reply #4 on: March 10, 2018, 09:56:30 pm »

I am trying to benchmark the staking interaction between nucleic acid base and amino acid side chain using SNAP. I think it will be easier for me to parse the information with json.

Best,
Honglue

Offline xiangjun

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Re: Implement Json
« Reply #5 on: March 10, 2018, 10:59:32 pm »
I could add this portion in JSON for you to try out, if you (1) let me know more details on the format, and (2) agree to provide me with feedback on how the SNAP algorithm is working.

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

Offline lvelve0901

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Re: Implement Json
« Reply #6 on: March 13, 2018, 02:30:50 pm »
Hi Xiangjun,

Thank you so much for your reply.

(1) Format:

I am thinking the similar format for DSSR should work great. If I remember it correctly, in DSSR json, you have an object called "hbonds" which you store all the hbonds pair right? For example:

Quote

[yuze@summer:dssr_learn] jq .hbonds[1] 6tna.json       
{
  "index": 2,
  "atom1_serNum": 20,
  "atom2_serNum": 1564,
  "donAcc_type": "standard",
  "distance": 2.663,
  "atom1_id": "N1@1:A.G1",
  "atom2_id": "N3@1:A.C72",
  "atom_pair": "N:N",
  "residue_pair": "nt:nt"
}


I think similar structure is fine. You can also add stacking interaction as a separate object in the json file.

By the way, in the introduction, you said

Quote
SNAP recognizes and outputs base-amino-acid H-bonding and stacking interactions.

Does that mean SNAP cannot output nucleic acid backbone interaction (only nucleic acid base)?

(2) Feedback:

I am currently training an undergraduate to analyze the interaction mode of RNA and protein. We will do the analyze for all the deposited protein RNA structures in RCSB. So we will definitely provide useful feedback when we encounter some wired cases.

Best,
Honglue




Offline xiangjun

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Re: Implement Json
« Reply #7 on: March 14, 2018, 02:28:42 pm »
Hi Honglue,

I've planned to add JSON output for SNAP when it reaches v1.0. Now you are interested in JSON output for "the staking [sic] interaction between nucleic acid base and amino acid side chain using SNAP". I was asking you for more details on the format of this part so I can tailor my effort to your specific need. What SNAP text output you want to be in JSON format? Please use a concrete example to make your point unambiguous.

Quote
Does that mean SNAP cannot output nucleic acid backbone interaction (only nucleic acid base)?

Please start a new thread. Again, using a concrete example so I can better understand what you mean.

Quote
I am currently training an undergraduate to analyze the interaction mode of RNA and protein. We will do the analyze for all the deposited protein RNA structures in RCSB.

You may want to try other available (and published) tools for analyzing RNA-protein interactions from PDB coordinates. SNAP is in beta testing version, after all.

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

 

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.