Messages

1

RNA structures (DSSR) / Re: DSSR could not install in my computor

« on: February 03, 2015, 08:24:02 am »

Dear Dr xiang-jun Lu
Thank you for kindness answer.
I installed DSSR program in my computer.
I will try to use DSSR program. 
(Um... additionally, I had installed x3dna program another computer using "VirtualBox"-Linux32bit. But I want to use Cygwin in Window 7. I bought new computer and Installed DSSR program according to your comments. Is it same method of installation x3dna program? )

I have another question.
Can I analysis DNA structure using DSSR program? (In this case, is 3DNA program more suitable?)
According to User manual and your lecture,
DSSR program only show structure of molecules or visualized graphic..
I almost finished two experiments, and I want to match my results using computer programs.

1. First, I want to analysis cohesive ends structure, which contain 5'- nick parts or non-Watson-Crick base(consist of 16 base pairs).
I have PDB files. Then, I tried to analysis using your programs. 
Firstly, I used x3dna program. However, program does not read my PDB files. (I added Image)
On the other hands, web DSSR program could read my PDB file.
(This is a reason that I tried to installed DSSR)
So, I am trying to use DSSR program to analysis DNA helical geometry and structures. (Angles, shapes, and so on.) If you have good advice, could you provide some guidelines??

2. Second, I want to analysis DNA Secondary structures. However, DSSR program does not provide Energy calculation and Molecular simulation results. (Actually… I want to get energy and stable shapes under different salt concentration)
Therefore, I plan to design and visualize secondary structures and predict possibility of DNA secondary structures.
In this case, Can I get additional results (energy or stability) using DSSR or 3DNA. Or are other programs more suitable?

Sorry, My English skill is too bad…. I afraid my questions were so rude or hard to understand.
Thank you for read my question.
From InHyun Song

2

RNA structures (DSSR) / DSSR could not install in my computor

« on: February 02, 2015, 01:02:40 am »

Dear developer Dr.Xiang-jun Lu,

Hello. I want to use 3DNA-DSSR calculating and analysizing of DNA structures.
However, I didn't install DSSR program. I used Window 7 and already installed Cygwin64 termial and  MinGW/MSYS.
I watched lecture Movie of DSSR  and read DSSR user manual. But there were no solution about my case.
Since I'm beginner computor program(like x3dna, Cygwin64, termial and so on.),
I don't know how to solve these problems.

1) I Installed and start Cygwin64. Next, I downloads DSSR program in 'Downloads folder'
    Next, accroding to your lecture, I typed 'mv ~/downloads/x3dna-dssr' . But, did not working.
    Message lik this : "mv: cannot stat 'home/abmi/Downloads/x3dna-dssr' : No such file or directory."

2) Then, I made 'X3DNA' Folder in 'cygwin64 folder', next, I moved 'x3dna-dssr' to that folder. (This case can be read)
    After entering X3DNA folder, I did same work accroding your lecture.
    Typing 'chmod u+x x3dna-dssr'     /   'ls –l'
    Then, before typing "-rwxr--r-x 1 abmi None 985566 February  2 12:20 x3dna-dssr.exe"
             After typing "-rwxr-xr-x 1 abmi None 985566 February  2 12:20 x3dna-dssr.exe"
 
    Next, I typed 'x3dna-dssr -v' and 'x3dna-dssr -h'.
    However, answer "-bash: x3dna-dssr: command not found"


Thank you so much,
InHyun Sin