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Messages - Mohit Chawla

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1
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
-------------------------------------------------------------------------------

2
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

3
RNA structures (DSSR) / Re: SASA of nucleobases
« on: February 06, 2020, 04:23:10 pm »
Hello,
Thanks, I will check it. I also found that Naccess software could also do this job.
Regards,
Mohit

4
RNA structures (DSSR) / SASA of nucleobases
« on: February 06, 2020, 01:35:47 am »
Hello,
May I know if we have the option in DSSR from which we can calculate the solvent accessible surface area of individual nucleobases of RNA structures?
Thanks
Mohit

5
RNA structures (DSSR) / Re: atom-base capping
« on: April 04, 2017, 10:27:34 am »
Thanks Xiang-Jun.
It is working.
Regards,
Mohit

6
RNA structures (DSSR) / Re: atom-base capping
« on: April 04, 2017, 12:07:26 am »
Dear Xiang-Jun,
Related to the atom-base capping interactions, I can see that such an interaction is detected with the distance of atom with the base plane of <= 3.5 A. However, if I want to detect such an interaction with distance > 3.5A, is it possible by the DSSR? If yes, please suggest me the option.
regards,
Mohit

7
RNA structures (DSSR) / Re: atom-base capping
« on: December 12, 2016, 02:43:44 pm »
Dear Xiang-Jun,

It is working now. Thanks very much.

Regards,
Mohit

8
RNA structures (DSSR) / Re: atom-base capping
« on: December 12, 2016, 04:57:30 am »
Dear Xiang-Jun,
Thanks for the reply. I tried to add --water ( or --h20) option, but it does not return the water-base contact.

Regards,
Mohit

9
RNA structures (DSSR) / atom-base capping
« on: December 11, 2016, 09:43:12 am »
Hi,
In the atom-base capping interactions, is it possible to also search for oxygen(water) to base contacts. For instance, in PDB id: 3d0u, HOH 213 makes a capping contact with G77, which we can not detect in the current version of dssr or may be I am missing with some option. Kindly suggest.
Thanks,
Mohit

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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.