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Author Topic: Problems with installing 3DNA on MinGW/MSYS  (Read 8286 times)

Offline kumutha

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Problems with installing 3DNA on MinGW/MSYS
« on: March 20, 2012, 09:59:53 pm »
Hi,

 Is it possible to install 3DNA software on windows XP? If so, how do I do it?  should I install MinGW or Cygwin? 

Offline xiangjun

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #1 on: March 20, 2012, 11:24:11 pm »
Yes, it is possible to install 3DNA on Windows XP -- the distributed v2.1beta-cygwin-win and v2.1beta-mingw-win were actually compiled on Windows XP. As to MinGW vs Cygwin, it is up to you: in my limited experience playing 3DNA on Windows, Cygwin seems more Linux-like, whilst MinGW is more Windows-like. If you are an experienced Windows user, you may try MinGW first.

Of course, if you have any technical problems, please post them here.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline kumutha

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #2 on: March 20, 2012, 11:30:15 pm »
Thank you.  :)

Offline Vandana

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #3 on: April 03, 2012, 12:49:40 pm »
I have installed the 3DNA v2.1beta MinGW/MSYS on windows 7. I have also installed ruby and MinGW as given in your previous post. I have extracted till bin. I have a problem with the x3dna_setup  command. It keeps showing an error as not recognized as internal or external command operable program or file. Can you tell me how to compile this and I also tried setting the environment variable from the control panel but it didn't work.
Thanking you

Vandana
 

Offline xiangjun

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #4 on: April 03, 2012, 01:45:28 pm »
Hi Vandana,

Sorry to hear your problem in setting up 3DNA on Windows 7 using MinGW/MSYS. To help identify where the problem is, please do the followings:
  • First, change into the 3DNA bin/ directory
  • Then type: pwd, what is the output?
  • What's the output of ruby -v?
  • If the above step runs successfully, what's the output of ruby x3dna_setup?

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Vandana

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #5 on: April 04, 2012, 01:17:56 am »
thankyou. I did execute the commands you posted
1. changed the bin to 3DNA bin
2. the pwd showed the following result 'pwd' is not recognized as an internal or external command,
operable program or batch file.
3. ruby -v showed ruby 1.9.3p125 (2012-02-16) [i386-mingw32]
4. ruby x3dna_setup showed : Unknown shell: not-set -- you've to set X3DNA and PATH manually:
             o set up the X3DNA environment variable
             o add $X3DNA/bin to your command search path
Regards
Vandana

Offline Vandana

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #6 on: April 04, 2012, 01:44:17 am »
I just tried to run the find_pair command and it did display a detailed command-line help then i tried the example given in the nature protocol paper and a PDB coordinate file  named 'multiplets.pdb was created.  :)
 

Offline xiangjun

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #7 on: April 04, 2012, 07:29:15 am »
Hi Vandana,

I am a bit surprised that you cannot run the basic 'pwd' (present working directory) command in you MinGW/MSYS -- Windows 7 system. Anyway, I'm glad to know that you've got 3DNA up and running; now you can start to play around with 3DNA. If you have any questions, do not heistate to post back on the forum!

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Vandana

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #8 on: April 04, 2012, 11:32:30 am »
Thankyou  :)

Offline Vandana

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #9 on: April 16, 2012, 12:15:12 pm »
Hi,

I have installed 3DNA on a windows platform. I can run all applications but have problem in running files like blocview etc. an error as 'blocview' is not recognized as an internal or external command,operable program or batch file keeps poping up. Could plz help me resolve the problem

Regards
Vandana.R

Offline xiangjun

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #10 on: April 16, 2012, 03:11:20 pm »
Thanks for using 3DNA and for posting your question on the forum.

It is a bit complicated to setup the environment to run blocview (especially on Windows), for two reasons:
You may be able to run blocview using Cygwin on Windows, but I've never tried it myself. Any comments from other users? In my experience, it is straightforward to use blocview on Linux or Mac OS X where such third-party components are readily available. In future releases of 3DNA (presumably starting from v2.2), blocview would alternatively take advantage of PyMOL.

Now back to your question, are you using MinGW/MSYS or Cygwin? Please give details about the error message, using copy-and-paste.

Xiang-Jun
« Last Edit: April 16, 2012, 03:51:59 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Vandana

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #11 on: April 17, 2012, 10:24:40 am »
Thankyou for the reply .I have installed MinGW/MSYS on my system. Apart from this i have also installed raster3d , pymol and Rasmol. The error msg that i get is " 'blocview' is not recognized as an internal or external command,operable program or batch file ". I have followed the steps as that given in the nature protocol paper. Will installing perl solve my problem to some extent ??

Regards
Vandana.R

Offline xiangjun

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #12 on: April 17, 2012, 11:10:49 am »
Thanks for providing your system info (MinGW/MSYS). The error message means either you do not have 3DNA installed properly, or the script blocview is not executable. Which version of 3DNA are you using?

Do the following and report back verbterm the output:

Code: [Select]
cd $X3DNA/bin
ls -al

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Vandana

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #13 on: April 19, 2012, 07:37:16 am »
As mentioned in my previous post the setup file did not run but the applications ran like find_pair etc. I have installed the  3DNA v2.1beta version on my systems. below is the out put that i got when i ran your command.
Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\triindia>cd C:\X3DNA\3DNA bin

C:\X3DNA\3DNA bin>cd $X3DNA/bin
The system cannot find the path specified.

C:\X3DNA\3DNA bin> ls -al
'ls' is not recognized as an internal or external command,
operable program or batch file.

Regards
Vandana.R

Offline xiangjun

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Re: Problems with installing 3DNA on MinGW/MSYS
« Reply #14 on: April 19, 2012, 07:54:44 am »
From the information you provided, 3DNA is clearly not properly setup in your Windows system. I was confused how you could run find_pair etc.

You said you used the compiled version of 3DNA for MinGW/MSYS, so why not you launch a MinGW Shell?
C:\Users\triindia>cd C:\X3DNA\3DNA bin
You have a directory named 3DNA bin? A space between 3DNA and bin?

In my MinGW Shell, this is the output from 3DNA v2.1beta setup script.
$ x3dna-v2.1beta/bin/x3dna_setup
Unknown shell: not-set -- you've to set X3DNA and PATH manually:
             o set up the X3DNA environment variable
             o add $X3DNA/bin to your command search path

Setting up 3DNA should be a straightforward process. If you have
technical problems, ask a local expert for help, or post them at
the 3DNA forum.

I installed 3DNA under directory $HOME/x3dna-v2.1beta. So I have created a text file (named set-me-up), with $X3DNA environment variable and X3DNA/bin path set explicitly as below:
Code: [Select]
export X3DNA=$HOME/x3dna-v2.1beta
export PATH=$X3DNA/bin:$PATH

Then I can run the following (note it is a dot at the beginning):
Code: [Select]
. set-me-up
and you will see the following when run the "blocview -h" command:
~ [237] blocview -h
===========================================================================
SYNOPSIS
    blocview [OPTION]... PDBFILE
DESCRIPTION
    Generates a schematic image which combines base block representation
    with protein ribbon. The image has informative color coding for the
    nucleic acid part and is set in the "best-view" by default. Users need
    to have MolScript, Raster3D and ImageMagick properly installed on their
    system.
        -o   use original coordinates contained in the PDB data file
        -j   output image in JPG format (default to PNG)
        -t[=]RESOLUTION   create PyMOL ray-traced image at RESOLUTION
        -d   display the generated image using "display" of ImageMagick
        -b   ball and stick model with filled base ring
        -c   clean up temporary common files
        -r   only backbone P atoms + base Ring atoms of nucleic acids
        -p   set the best view based on Protein atoms
        -a   set the best view based on All atoms
        -s[=]NUM    set scale factor for the image
        -i[=]IMAGE  set image file name (default to t.png)
        -x|y|z=ANGLE  rotation around x, y, or z-axis by ANGLE degrees
        PDBFILE   a PDB data file name (other than 't.pdb')
EXAMPLES
    blocview -d -i=bdl084.png bdl084.pdb
AUTHOR
    3DNA v2.0 [June 8, 2008] (by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com)
    Check URL: http://x3dna.org/ for the latest
===========================================================================

If the instruction still does not make sense to you, your best bet may be to consult a local expert for setting up 3DNA. Alternatively, you can try w3DNA: the web-interface to commonly used functionality of 3DNA.

Xiang-Jun
« Last Edit: April 19, 2012, 02:18:07 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.