Implement Json

xiangjun:
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

lvelve0901:
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"
}

--- End quote ---

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.

--- End quote ---

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

xiangjun:
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)?
--- End quote ---

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.
--- End quote ---

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

kyle_:
Hello,
I am using SNAP via `x3dna-dssr snap -i=my_file.pdb` and have found the output very useful, but am hoping to export it as JSON to automate some of my analysis. I see how I can run `x3dna-dssr -i=my_file.pdb --json`, and it seems that when `x3dna-snap` was packaged separately it had also a `--json` flag for this purpose (eg. https://x3dna.org/articles/h-bonds-reported-by-dssr-and-snap). Such a flag no longer seems to work with `x3dna-dssr snap -i=my_file.pdb --json`, so I am asking: does this JSON format functionality still exist for SNAP output? Perhaps it exists and this flag is not the way to access it.

xiangjun:
Hi,

Thanks for using SNAP/DSSR and for posting your question on the Forum.

The --json option is available in the DSSR Pro version (x3dna-dssr snap --json) . This is one of the few features that is currently not enabled in the free DSSR Basic Academic version. No paper on SNAP has been published yet. Some features need further developments and better documentation. I may consider enable more Pro features in the Basic version in the future.

The general principle of 3DNA/DSSR is to ensure that published results and documented features (in the DSSR Manual) are reproducible. DSSR has more to offer than those published/documented.

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