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Author Topic: have no output  (Read 934 times)

Offline Trista

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have no output
« 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?

Offline xiangjun

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Re: have no output
« Reply #1 on: January 17, 2017, 03:09:07 pm »
Hi,

I've tried SNAP on 1ffk and did not find any H-bonds between proteins and RNA, as you reported. However, trying SNAP on 1s72 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.
« Last Edit: January 17, 2017, 03:33:02 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: have no output
« Reply #2 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

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

Offline Trista

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Re: have no output
« Reply #3 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]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.