3DNA Forum

Questions and answers => DNA/RNA-protein interactions (SNAP) => Topic started by: Trista on January 17, 2017, 01:49:25 pm

Title: have no output
Post by: Trista on January 17, 2017, 01:49:25 pm: hi,
i run `snap --get-hbonds -i=1FFK.pdb -o=1.snap` hoping to figure out interactions between the a.a and RNA.
log reported as below:

Processing file '1FFK.pdb' [1FFK]

Time used: 00:00:00:03

But I cannot get my output,1.snap,why?There is no hbonds within this structure?
Title: Re: have no output
Post by: xiangjun on January 17, 2017, 03:09:07 pm: Hi,

I've tried SNAP on 1ffk (http://www.rcsb.org/pdb/explore/explore.do?structureId=1ffk) and did not find any H-bonds between proteins and RNA, as you reported. However, trying SNAP on 1s72 (http://) reports 1749 H-bonds. So I guess it must be due to atomic coordinates issue with 1ffk. You may want to dig into 1ffk deeper to understand why, but I believe SNAP is doing its job as designed.

Hope this help.

Xiang-Jun

Did you know that you could also use DSSR with JSON output to easily parse H-bonds?

Code: [Select]
x3dna-dssr -i=1oct.pdb --json | jq '.hbonds[] | select(.residue_pair == "nt:aa")'
The underlying algorithm for H-bond detection is the same for DSSR and SNAP, with the default text output tailored to nt:nt and nt:aa respectively. With the DSSR --json option, 'ALL' H-bonds are reported. In the near future, the --json will be available to SNAP as well.
Title: Re: have no output
Post by: xiangjun on January 17, 2017, 05:31:44 pm: As a follow-up, I've checked the coordinates file 1ffk.pdb. As shown below, only CA atoms are present for the protein components. That explains why no H-honds are detected by SNAP at the protein-RNA interface.

Code: [Select]
ATOM 60615 CA GLY A 1 90.042 119.507 70.725 1.00 19.43 C ATOM 60616 CA ARG A 2 91.130 122.831 69.274 1.00 20.79 C ATOM 60617 CA ARG A 3 94.149 123.627 67.107 1.00 20.95 C ATOM 60618 CA ILE A 4 97.217 124.158 69.269 1.00 22.45 C ATOM 60619 CA GLN A 5 99.055 127.467 68.965 1.00 21.75 C ATOM 60620 CA GLY A 6 101.878 126.130 66.843 1.00 20.71 C ...
Best regards,

Xiang-Jun
Title: Re: have no output
Post by: Trista on January 17, 2017, 09:22:15 pm: Thank you so much!
I will try another rRNA structure!