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Author Topic: install xdna on linux  (Read 118 times)

Offline sima

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install xdna on linux
« on: August 04, 2019, 07:35:20 am »
hi
I have a windows/linux platforms
I want to install x3dna on my linux .but Nothing happens when I use this command
export X3DNA='/home/sima/x3dna-v2.4'
  export PATH='/home/sima/x3dna-v2.4/bin':$PATH


sima@HP:~/x3dna-v2.4/bin$ export X3DNA='/home/sima/x3dna-v2.4'
sima@HP:~/x3dna-v2.4/bin$ export PATH='/home/sima/x3dna-v2.4/bin':$PATH
sima@HP:~/x3dna-v2.4/bin$ source ~/.bashrc


I didn't understand the text below before executing the commands
for your 'bash' shell, add the following into ~/.bashrc:
« Last Edit: August 04, 2019, 08:15:41 am by sima »

Offline xiangjun

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Re: install xdna on linux
« Reply #1 on: August 04, 2019, 10:52:24 am »
In your current settings, what happens when you run: find_pair -h?

Change to the directory when 3DNA is installed, then type: pwd. What is the result?

What is the output of: echo $SHELL

Xiang-Jun
« Last Edit: August 04, 2019, 10:54:04 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline sima

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Re: install xdna on linux
« Reply #2 on: August 04, 2019, 05:38:43 pm »
It executes when I run the following command in the terminal I opened for installation,
sima@HP:~/x3dna-v2.4/bin$ pwd
/home/sima/x3dna-v2.4/bin

sima@HP:~/x3dna-v2.4/bin$ ./x3dna_setup
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
To install X3DNA, do as follows:
  (0) download the 3DNA distribution for your operating system from URL
          http://x3dna.org/
  (1) tar pzxvf x3dna-v2.4-linux-64bit.tar.gz
          # here for the 3DNA v2.4 distribution on 64-bit Linux
  (2) cd x3dna-v2.4/bin
  (3) ./x3dna_setup
          to run X3DNA, you first need to do two things:
              o set up the X3DNA environment variable
              o add $X3DNA/bin to your command search path
          for your 'bash' shell, add the following into ~/.bashrc:
          --------------------------------------------------------------
              export X3DNA='/home/sima/x3dna-v2.4'
              export PATH='/home/sima/x3dna-v2.4/bin':$PATH
          --------------------------------------------------------------
          and then run: source ~/.bashrc
  (4) to verify your installation, type: ./find_pair -h
          you should see some command-line help message
Problems? Visit the 3DNA Forum at URL http://forum.x3dna.org/howtos/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
sima@HP:~/x3dna-v2.4/bin$ export X3DNA='/home/sima/x3dna-v2.4'
sima@HP:~/x3dna-v2.4/bin$ export PATH='/home/sima/x3dna-v2.4/bin':$PATH
sima@HP:~/x3dna-v2.4/bin$ source ~/.bashrc
sima@HP:~/x3dna-v2.4/bin$ ./find_pair -h
===========================================================================
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-order base associations
        -a      read in only the 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, or combined
EXAMPLES
        find_pair sample.pdb sample.inp
        find_pair -p sample.pdb allbp_list
        find_pair -c+ sample.pdb sample_c+.inp
                  [then run: Cur+ < sample_c+.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 v2.4.3-2019apr06, created and maintained by xiangjun@x3dna.org

Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/
Please check 'http://x3dna.org/citations' on how to cite 3DNA --- THANKS!
===========================================================================
sima@HP:~/x3dna-v2.4/bin$ echo $SHELL
/bin/bash


but when I close the terminal I can't call the software.
sima@HP:~$ ./find_pair -h
bash: ./find_pair: No such file or directory
sima@HP:~$ cd x3dna-v2.4/bin
sima@HP:~/x3dna-v2.4/bin$ ./find_pair -h
Please set the X3DNA environment variable
Run 'x3dna_setup', and visit http://forum.x3dna.org/ for more info.

« Last Edit: August 04, 2019, 06:04:46 pm by sima »

Offline xiangjun

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Re: install xdna on linux
« Reply #3 on: August 04, 2019, 09:13:26 pm »
You need to add the two lines:

Code: [Select]
export X3DNA='/home/sima/x3dna-v2.4'
export PATH='/home/sima/x3dna-v2.4/bin':$PATH

into your ~/.bashrc file so that you can access 3DNA commands each time you open a new terminal window.

Or, you can place the two lines into a file, and then source that file each time you open a new terminal window.

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

 

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.