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Topics - sima

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1
General discussions (Q&As) / 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:

2
General discussions (Q&As) / examples
« on: June 29, 2019, 10:26:23 am »
hi
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

3
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

4
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
triplex-C10C10C10.pdb
triplex-C10C10C10.out
    2         # duplex
    0         # number of base-pairs

Time used: 00:00:00:00



i use this link
https://x3dna.org/highlights/pauling-triplex-model-of-nucleic-acids-is-available-in-3dna


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.