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Messages - sima

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General discussions (Q&As) / Re: install xdna on linux
« 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

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

  (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
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
        find_pair - locate base-pairs and helical regions
        find_pair [OPTION] PDBFILE OUTFILE
        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)
        PDB data file
        One-letter options can be in either case, any order, or combined
        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]
        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
        analyze, cehs, anyhelix, ex_str, stack2img
        3DNA v2.4.3-2019apr06, created and maintained by

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

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 for more info.

General discussions (Q&As) / install xdna on linux
« on: August 04, 2019, 07:35:20 am »
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:

General discussions (Q&As) / examples
« on: June 29, 2019, 10:26:23 am »
im following the example of triple helix in x3dna
When I use this command :

 find_pair -p fiber31.pdb fiber31.bps

This error is displayed:

handling file <fiber31.pdb>
open_tmpfile() failed: Permission denied

General discussions (Q&As) / 3dna tutorial
« on: May 27, 2019, 12:15:48 pm »
hi dr.xiangjun
im a new user of 3dna software
Sorry to take your time
I'm going to design a single-stranded DNA structure for designing the switches that work with the pH.
Do you have a file for full software training? Especially for the design of clamp switches.
I want to fully understand rebuild and mutate analysis of this software.
Does this software give us the possibility of protonizing the structure?
thanks for your help

General discussions (Q&As) / Re: design triple helix
« on: May 27, 2019, 10:49:29 am »
Hi Dr.xiangjun and mauricio esguerra :) :)
Thank you for your help and advice.
But I want to design triplex with my own sequence and turn it into a clamp switch. Like this article :

General discussions (Q&As) / design triple helix
« on: May 21, 2019, 02:59:19 am »
Hello . I am a new user
I reviewed the questions of others. Unfortunately, I did not understand how to design triple helix. Using fiber -pauling , I succeeded in making triple helix . But When I use find_pair command, the software shows the following text:
C:\Users\Sima>find_pair triplex-C10C10C10.pdb

handling file <triplex-C10C10C10.pdb>
no base-pairs found for this structure
    2         # duplex
    0         # number of base-pairs

Time used: 00:00:00:00

i use this link

thanks for your help

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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.