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

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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!

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.