Messages

1

General discussions (Q&As) / Re: How to read the out put file of 3DNA

« on: August 19, 2016, 12:54:03 pm »

Okay thank you very much Sir!

2

General discussions (Q&As) / Re: How to 3DNA set environment variables on Linux?

« on: August 18, 2016, 09:39:43 am »

Thank you Sir!
I was able to install 3DNA..

3

General discussions (Q&As) / Re: How to read the out put file of 3DNA

« on: August 18, 2016, 09:38:39 am »

Thank you Sir!
What I exactly want to know is what does it mean by this?
1>-:...2_:[.DA]A-----T[.DT]:..11_:-<...1
Is DA and DT denote the base plane of Adenine and Thymine respectively and can you please explain me what are those numbers??

4

General discussions (Q&As) / How to read the out put file of 3DNA

« on: August 18, 2016, 01:29:33 am »

Hi,
Does anyone know how to read the information of RMSD of the bases of out file?? I'm sorry I'm new to 3DNA  and I have no clue what it says.
This is the out put file that i got.

RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.046) ...1>-:...2_:[.DA]A-----T[.DT]:..11_:-<...1 (0.038)     |
   2   (0.051) ...1>-:...3_:[.DT]T-----A[.DA]:..10_:-<...1 (0.076)     |
   3   (0.036) ...1>-:...4_:[.DT]T-----A[.DA]:...9_:-<...1 (0.041)     |
   4   (0.052) ...1>-:...5_:[.DG]G-----C[.DC]:...8_:-<...1 (0.041)     |
   5   (0.057) ...1>-:...6_:[.DG]G-----C[.DC]:...7_:-<...1 (0.032)     |
   6   (0.038) ...1>-:...7_:[.DC]C-----G[.DG]:...6_:-<...1 (0.095)     |
   7   (0.056) ...1>-:...8_:[.DC]C-----G[.DG]:...5_:-<...1 (0.045)     |
   8   (0.097) ...1>-:...9_:[.DA]A-----T[.DT]:...4_:-<...1 (0.050)     |
   9   (0.066) ...1>-:..10_:[.DT]T-----A[.DA]:...3_:-<...1 (0.068)     |
  10   (0.055) ...1>-:..11_:[.DG]G-----C[.DC]:...2_:-<...1 (0.043)     |
  11   (0.032) ...1>-:..12_:[.DC]C-----G[.DG]:...1_:-<...1 (0.051)     |

Thank you in advance!!

5

General discussions (Q&As) / Re: How to 3DNA set environment variables on Linux?

« on: August 04, 2016, 03:08:35 am »

Hi Sir,
Thank you for your quick reply.
I followed the instructions as you've mentioned but when I typed find_pair -h or ./find_pair -h the following messages were displayed.
Also when I saved   setenv X3DNA '/home/xiangjun/x3dna-v2.1'
                                     setenv PATH '/home/xiangjun/x3dna-v2.1/bin':$PATH  in .cshrc file and entered source ~/.cshrc, these messages were displayed.
                                      No command 'setenv' found, did you mean:
                                      Command 'netenv' from package 'netenv' (universe)
                                      setenv: command not found

Can you please help me with that??

6

General discussions (Q&As) / How to 3DNA set environment variables on Linux?

« on: August 03, 2016, 11:25:26 am »

Hi,
The step 3 of installation on linux is not clear to me. What does it mean by set the environment variable X3DNA and add $X3DNA/bin to your command search path???
Im really looking forward to your reply.
Thank you!!