DSSR could not install in my computor

[songinhyun]

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

[xiangjun]

Dear InHyun Sin,

Thanks for your interest in using DSSR! I am sorry for the difficulties you experienced in trying to install the software. By design, DSSR takes a minimum approach from a user's perspective to get up and running. Indeed, you are first (I am aware of) in its nearly two-year release history to have issues even to get started. Yet, your case represents a 'dark corner' scenario for a beginner to computer programs in a Windows environments that I am not that familiar with (I routinely use Mac OS X and Linux). Let's work together to help you out -- it should not be that hard!

From your screenshots, you did download the Windows version of DSSR (named "x3dna-dssr.exe"), but put it in the wrong location. For the sake of illustration of a fresh install, please delete your downloaded copy of DSSR, and repeat the following steps:

• Using IE (Internet Exploring) or Chrome, log in to the 3DNA Forum to download the DSSR version labeled "Windows (compiled in MinGW/MSYS, works under DOS and Cygwin)". This DSSR executable "x3dna-dssr.exe" will be put into the default Downloads folder under your Window home directory (See attached screenshot on a Windows7-x64 machine).
• Double-click the "Cygwin64 Terminal" icon on your Desktop to open a new Cygwin terminal window, then follow the 6-step instructions of the second screenshot in red. In step#4, do not forget the dot at the very end '.'!

Please let me know how it goes.

Xiang-Jun
If you are familiar with Windows, you can click and drop the DSSR executable "x3dna-dssr.exe" into a folder on your Windows command path. The DSSR Windows version runs on "native Windows, Cygwin, and MinGW".

[songinhyun]

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

[xiangjun]

Hi  InHyun Song,

Thank you for kindness answer.
I installed DSSR program in my computer.
I will try to use DSSR program. 

Glad to hear that you've got DSSR up and running!

(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? )

You can install 3DNA v2.1 on Cygwin in Windows 7. See the post "How to install 3DNA on Linux and Windows?" for details.

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.

You can get some base pair parameters with DSSR by specifying the --more option. Check also "dssr-torsions.txt" for backbone conformational parameters. For more detailed analyses of your DNA structures, please use 3DNA v2.1.

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??

Several points here. From your screenshot, you have installed 3DNA (an old version?) successfully. After running find_pair, you need to run "analyze" to get the results. Please install 3DNA v2.1-2014dec22 -- run "find_pair -h" to verify your installation.

Please spend some time getting familiar on how 3DNA works. The manual "x3dna_v1.5.pdf" is a bit dated, but its contents are still valid. Please go over it. Read also the 2003 3DNA NAR paper, and repeat the recipes in the 2008 Nature Protocols paper.

I cannot give you a concrete answer as to how to analyze the 5'-nick parts not involved in Watson-Crick pairs. DSSR provides base stacking and H-bonding interactions, plus backbone conformational parameters you may find useful. The find_pair program in 3DNA v2.1 has a -s option for single-standed structure.

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?

DSSR and 3DNA v2.1 are for RNA/DNA structural analyses, with no functionality for energy calculations, predictions, or molecules dynamics simulations. From my understanding, you may find AMBER better suits your needs.

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

You are welcome for asking any DSSR/3DNA-related questions on the Forum. We all started as beginners for certain areas. It takes time and effort to become more experienced, and there is no end in learning.

In the future, please consider to start a new topic for a specific question. This thread, for example, was intended for issues related to DSSR installation, but it now covers many more topics and become less focused.

Best regards,

Xiang-Jun