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How to set up 3DNA on Windows
xiangjun:
3DNA v2.3 and previous versions contain a suite of programs, and associated data files. Setting up 3DNA is intended to be a simple process for those with command-line experience: it entails creating an environment variable named X3DNA to point to where 3DNA is stored, and an updated PATH that includes the $X3DNA/bin directory. The whole process is facilitated by a Ruby script, x3dna_setup, and should take no more than a few minutes.
With Linux and Mac OS, setting up 3DNA has normally not been an issue. For Windows, however, the situation is more complicated than desired. Cygwin or MinGW/MSYS is the preferred way to run 3DNA on Windows, but each requires the installation of a big package and the ending environment is not familiar to Windows users. By far, the most frequent and longest threads on the Forum are on how to properly set up 3DNA on Windows, initiated by new users who have no experience in command-line interface.
As of 3DNA v2.3.1-2017jun24, the compiled .exe files in the tarball x3dna-v2.3-mingw-win.tar.gz should run in native Windows (i.e. without Cygwin or MinGW/MSYS) via the command prompt. However, the default Windows command prompt (cmd.exe) is a dinosaur and awkward to use. I played with Windows PowerShell a bit, but it gave some surprises with processing of command-line options. The win-bash shell may be a choice, or one can install Bash on Windows 10.
In the long run, when the 'Bash on Windows' becomes a default, the whole issue of setting 3DNA will on longer exist any more. In the meantime, this FAQ entry provides detailed instruction on how to set up 3DNA v2.3 on native Windows (tested on Windows 7).
* Install ConEmu (Stable, Installer) -- it is far superior to Windows cmd.exe
--- Quote ---ConEmu-Maximus5 is a Windows console emulator with tabs, which presents multiple consoles and simple GUI applications as one customizable GUI window with various features...file and archive management, command history and completion, powerful editor.
--- End quote ---
* Download the Windows version of 3DNA v2.3, the x3dna-v2.3.zip file (Note that you need to register and log in to see the download link). The zip file normally ends up in the Downloads/ folder under your home folder (e.g., C:\Users\xiangjun\Downloads.)
* Right-click the x3dna-v2.3.zip file, in the context menu select "Extract All...". In the setting window, you can select the folder under which 3DNA will be installed. Please do not specify x3dna-v2.3 explicitly in setting the folder, since x3dna-v2.3 will always be appended to it.
In principle, you can install 3DNA anywhere. It is a good choice to put it directly under your home folder (e.g., C:\Users\xiangjun). See the screenshot below.
Click the "Extract" button at the bottom right. You'll see lots of files being extracted. Take a note of the 3DNA folder (i.e., C:\Users\xiangjun\x3dna-v2.3\ as shown above) as this information is needed next.
Navigate to the designated 3DNA folder and make sure it has the content shown below. Right-click on file license.txt and select "Properties". The Location: field should report its parent folder (no ending slash) that agrees with the one shown above.
* Set the X3DNA environment variable and update the PATH. See "How to set the path and environment variables in Windows" for details. Here I am using Windows 7 as an example.
* From the "Desktop", right-click the "Computer" icon and select "Properties". If you don't have a Computer icon on your desktop, click the "Start" button, right-click the "Computer" option in the Start Menu, and select "Properties".
* Click the "Advanced System Settings" link in the left column.
* In the System Properties window, click on the "Advanced" tab, then click the "Environment Variables..." button near the bottom of that tab.
* In the Environment Variables window, the top part is for User variables (for xiangjun in the example). Click the "New..." button, and you will see the New User Variable window. For the Variable name text field, type X3DNA, and for Variable value, type C:\Users\xiangjun\x3dna-v2.3\ (with ending slash). Note that this value must match what is specified in the extraction step, i.e., pointing to where 3DNA is actually installed. See the following screenshot.
Click the "OK" button, and the result is as shown below:
* In the Environment Variables window, the bottom part is for System variables. Scroll to find the Path variable, which contains a long list of values separated by semicolon (e.g. C:\Windows\system32;...). Highlight (select) the Path entry and click the "Edit..." button. The Edit System Variable window will appear. The Variable name text field will be Path. Scroll to the end of Variable value, add ;C:\Users\xiangjun\x3dna-v2.3\bin. Note that each different directory is separated with a semicolon. See screenshot below.
* Now double-click the ConEmu icon on the desktop to open a new terminal window. Type find_pair -h in the command prompt, you should see a result screen as shown below.
* Optionally, install Ruby on Windows. You may skip this step when you just get started with 3DNA on Windows. The Ruby scripts distributed with 3DNA v2.3 are mostly for generating schematic block images, and analyzing NMR ensembles.
Do not forget to click the check box "Add Ruby executables to your PATH". See the first entry in Troubleshooting.
Note that at the end of the installation, you do not need to click the checkbox to install "MSYS2 and development toolchain". 3DNA v2.3 runs just fine as is, even though getting them installed does not hurt.
If you notice any problem, please post below with details.
Hari Seldon:
I installed on Windows and got to the end just fine until find_pair -h
linux@DESKTOP-JS6SA18 C:\Users\linux
> find_pair -h
'find_pair' is not recognized as an internal or external command,
operable program or batch file.
I also tried installing 3DNA On Linux (including Mac OS X, or Cygwin on Windows)
http://forum.x3dna.org/howtos/how-to-install-3dna-on-linux-and-windows/
And it all worked until find_pair -h
linux@DESKTOP-JS6SA18 /cygdrive/d/Documents/NYU/Projects/Gunsalus/Code/3DNA/Linux/x3dna-v2.3/bin
$ ./find_pair -h
-bash: ./find_pair: cannot execute binary file: Exec format error
xiangjun:
--- Quote ---> find_pair -h
'find_pair' is not recognized as an internal or external command,
operable program or batch file.
--- End quote ---
The error message means that the PATH is not set properly. Probably the X3DNA environment variable is not set correctly either.
I've just finished the FAQ, with corrections with initial draft versions. You may be following an early version of the post. Could you please try again, following the steps, and report back if it works? Please use screenshot as necessary.
Also, what Windows version are you using?
Best regards,
Xiang-Jun
Hari Seldon:
I am using Windows 10.
Download ConEmu Stable, Installer (32-bit, 64-bit) - 5.23 MB | version: 161206 | File Signatures
Ruby 2.4.1-2 (x64)
RubyInstaller2
Download the Windows version of 3DNA v2.3, the x3dna-v2.3.zip file
Set the X3DNA environment variable and update the PATH
xiangjun:
Thanks for the detailed screenshots. It is weird. Things should not be that hard. Let's work together to sort things out.
Could you please do the following:
* Within ConEmu terminal, type: echo %X3DNA%
* On my case, the output is: C:\Users\xiangjun\x3dna-v2.3\, as originally set.
What's your output?
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
