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Questions and answers => General discussions (Q&As) => Topic started by: espinosaleal on February 22, 2013, 07:30:05 am

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Title: one comment + one question
Post by: espinosaleal on February 22, 2013, 07:30:05 am

Hi everybody

I've been using X3DNA (v2.1) the last days trying to learn how to build up some structures and I'm
really happy, there are a lot of things that i can do with this tool. Anyway, I have one comment and
one stupid question:
1. Comment: the option -single doesn´t work properly, you have to use -s instead.
2. Stupid question: how I can add the hydrogen atoms to my structure? Maybe there is
    a better way to do it than using for example Avogadro, because if you use this option
    the sistem also add the hydrogen atoms to the backbone.

Thanks a lot,

leonardo

Title: Re: one comment + one question
Post by: mauricio esguerra on February 22, 2013, 07:54:34 am

Hi Leonardo,

You can use -s or -1, as options to treat the nucleic acid structure as a single strand.
From find_pair help you get:

Code: [Select]

===========================================================================
NAME
        find_pair - locate base-pairs and helical regions
SYNOPSIS
        find_pair [OPTION] PDBFILE OUTFILE
DESCRIPTION
        locate base-pairs and helical regions given a PDB data file. Its
        output can be directly fed into analyze, cehs and Lavery's Curves
        program.
        -s, -1  treat the whole structure as a continuous single helix.
                Useful for getting all backbone torsion angles
        -c      get Curves input for a duplex
        -c+     get input for Curves+ (duplex, ATOM records only)
        -d      generate a separate output file for each helical region
        -p      find all base-pairs and higher base associations
        -a      read in only ATOM records, ignoring HETATM records
        -z      more detailed base-pairing information in the output
        -h      this help message (any non-recognized options will do)
INPUT
        PDB data file
        One-letter options can be in either case, any order and combined
EXAMPLES
        find_pair sample.pdb sample.inp
        find_pair -p sample.pdb allbp_list
        find_pair -c sample.pdb sample_curves.inp
OUTPUT
        base-pair listing for input to analyze, cehs and Curves
        bestpairs.pdb, hel_regions.pdb, col_chains.scr, col_helices.scr
        allpairs.pdb, multiplets.pdb, mulbp.inp
SEE ALSO
        analyze, cehs, anyhelix, ex_str, stack2img
AUTHOR
        3DNA v2.1 (c) 2012 Dr. Xiang-Jun Lu (http://x3dna.org)
===========================================================================

To add hydrogens I use pymol.
You can just issue the

Code: [Select]

h_add command and it will correctly add hydrogens.
http://www.pymolwiki.org/index.php/H_Add (http://www.pymolwiki.org/index.php/H_Add)

You can even choose a selection to decide which unfilled valence area you want to populate with hydrogens.

Cheers,

M.

Title: Re: one comment + one question
Post by: xiangjun on February 22, 2013, 11:46:49 am

Hi Leonardo,

Thanks for using 3DNA, and posting your comment & question on the forum. User-feedback is one of the driving forces to make 3DNA a better tool to serve the community.

Quote

1. Comment: the option -single doesn´t work properly, you have to use -s instead.

Since you mentioned to "build up some structures", I guess you mean the fiber -single option. Indeed, you've identified an inconsistency in the command-line documentation vs how the program actually runs. I've fixed the issue, so now you can use -si, -single, -single-strand or -s for the same effect. Please download the updated 3DNA v2.1 release dated 2013feb22.

This is a concrete example how a user like you help improve 3DNA -- thanks!

Quote

2. Stupid question: how I can add the hydrogen atoms to my structure? Maybe there is
    a better way to do it than using for example Avogadro, because if you use this option
    the sistem also add the hydrogen atoms to the backbone.

In addition to what esguerra suggested, you may also try the "Reduce Software for Adding Hydrogens (http://kinemage.biochem.duke.edu/software/reduce.php)" from the Richardson laboratory.

HTH,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University