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Author Topic: H-bonding between RNA bases and protein amino acids  (Read 107 times)

Offline Mohit Chawla

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H-bonding between RNA bases and protein amino acids
« on: September 02, 2020, 07:38:28 am »
Hi,
May I know if we can calculate the possible H-bonding pairing between the RNA nucleobases and amino acids in RNA-Protein complexes using the current version of SNAP?
Thanks
Mohit

Offline xiangjun

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Re: H-bonding between RNA bases and protein amino acids
« Reply #1 on: September 02, 2020, 12:04:13 pm »
Hi Mohit,

What "current version of SNAP" did you refer to? Have you tried "x3dna-snap --help"? Please post back the output of running this SNAP command option.

Best regards,

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

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Offline Mohit Chawla

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Re: H-bonding between RNA bases and protein amino acids
« Reply #2 on: September 03, 2020, 06:24:40 am »
Hello,
Thanks for your suggestion.
Actually, I was using the web version of  SNAP; http://snap.x3dna.org/ and it was not working for PDB files of ribosome structures. Then, I noticed that it has a limitation of uploading PDB files with less than two megabytes (2mb) in size.
Now I have downloaded the SNAP and i seems to be working.. Thanks. I post back the output as you requested below:
------------------------------------------------------------
Usage: x3dna-snap [options]

Each option is specified via --key[=val] (or -key[=val] or key[=val];
i.e., two/one/zero preceding dashes are all accepted), where 'key' can
be in either lower, UPPER or MiXed case. Options can be in any order.
Options:
  --help         Print this command-line help information (-h)
  --version      Print version number and exit (-v)
  --citation     Print preferred citation(s) and exit (--cite)
  --input=file   Specify a PDB/mmCIF file for analysis (-i=file)
  --output=file  Designate the main SNAP output file (-o=file) [stdout]
  --json         Generate output in JSON format for easy parsing
  --cutoff=float Set the distance cutoff between interacting aa/nt [4.5]
  --type=string  Select interacting nt moiety: base|backbone|both|either [either]
  --t-shape      Output T-shaped contacts between planar moieties
  --interface    Summarize each nucleotide with its contacted amino acids
  --methyl-C     Check interactions between DNA 5mC and protein side chains
  --get-hbonds   Find H-bonds at the interface of protein and nucleic acid
            with --get-hbonds-nucleic to include H-bonds within DNA/RNA
            with --get-hbonds-protein to include H-bonds within protein
            with --get-hbonds-nucleic-protein to include H-bonds in both
  --auxfile      Produce numerous auxiliary files (e.g. A-arg.pdb)
  --nmr          Process an ensemble of NMR structures
  --cleanup      Remove common files with fixed names and exit

Examples:
  x3dna-snap -i=1oct.pdb
  x3dna-snap -i=1oct.pdb --json
  x3dna-snap -i=2err.pdb --nmr -o=2err-model.out
======================================================================
Questions, comments, or suggestions?
  Please visit the 3DNA Forum (http://forum.x3dna.org) for help.

Time used: 00:00:00:00
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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.