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DNA/RNA-protein interactions (SNAP) / Re: H-bonding between RNA bases and protein amino acids
« 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
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------