6 Sep 2009

VMD Package Builder for Ubuntu and Debian

What is VMD?

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

Text above is copied from Official VMD Site

How build process of VMD Ubuntu package looks like?

$ bash vmd-package.sh vmd-1.8.7.src.tar.gz
Options chosen depends on this packages in Debian/Ubuntu

build-essential csh libstdc++5 libc6 libcc perl libglu1-mesa mesa-common-dev libgl1-mesa-dri libgl1-mesa-glx libglu1-mesa-dev xlibmesa-gl-dev fontconfig tk8.5-dev tk8.5 tcllib libfltk1.1 libfltk1.1-dev libxft2 libxft-dev python-netcdf python2.5 python2.5-dev libnetcdf-dev libnetcdf4 python-numpy

This script doesn't support resume!!!
If some packages are missing, you should run apt-get install command
Continue? [Y] - YES/ [N] - NO
y

#############################################################
12:51:34 Starting building process on vmd-1.8.7.src.tar.gz
#############################################################

12:51:35 Unpacking sources from vmd-1.8.7.src.tar.gz
12:52:13 Starting compilation of plugins. This may take a while ...
12:57:46 Compilation of plugins successful
         Copying plugins to /home/johny/Pulpit/vmd/vmd-deb/usr/local/lib/vmd/plugins/
12:57:53 Compilation of plugins completed successfully.
12:57:53 Starting build of VMD. This may take a while ...
         Running configure
         using configure.options: LINUX MESA TK TCL PTHREADS FLTK PYTHON NETCDF NUMPY
         Correcting Makefiles
         Starting compilation of main VMD program, this may take a while
         Compilation done.
         Starting copying of files to /home/johny/Pulpit/vmd/vmd-deb/
         Copying done.
13:03:33 Build process completed successfully

#############################################################
13:03:33 Starting build process of *.deb package
#############################################################

13:03:33 Creating and correcting misc stuff
         Patching files. (vmd)
         Creating VMD icon
         Making Debian Menu Entry
         Adding mime-support info
         Creating freedesktop.org desktop entry
         Adding freedesktop.org shared mime info entry
         Adding KDE MIME database entry
         Copying documentation ...
         Adding postinst and postrm scripts
         Generating control file
         Calculating MD5 sums
13:05:56 Building *.deb package
         13:06:44 Cleaning
13:07:11 Completed successfully. Package is ready to install.

To perform install run as root:
 dpkg -i vmd_*.deb

Where I can find Debian/Ubuntu vmd package builder?

Source can be obtained on my Google Code account.

How to use it?

  1. Download VMD sources from Official VMD page
  2. Download VMD package builder using command: wget http://0x1fff.googlecode.com/svn/trunk/public-projects/vmd-package-builder/vmd-package.sh
  3. Type in terminal: bash vmd-package.sh vmd-*.*.*.src.tar.gz
  4. Hit enter and read stuff on screen carefully

It's not working, what should I do?

  • Check if are dependencies are installed
  • Check version of VMD, and compare it with tested versions on begining of script
  • If there is a build problem with version lower than 1.8.7 it will not be probably fixed
  • Checkout "known bugs" and comments in this post
  • If you know how to fix it - just do it and send me path
  • If you do not know - write a comment below - bug report should be like this:
    Hello! :) I've found a bug in vmd-package.
    
    my Ubuntu/Debian version is: VERSION HERE
    my PC architecture is: ARCH HERE (if you don't know it's probably x86)
    my vmd-package version is: VERSION HERE
    my VMD version is: VMD VERSION HERE
    I'm trying to build VMD with these settings (compilation options): OPTIONS HERE
    I'm getting output like: OUTPUT HERE
    
    Here are compressed log directory: http://...URL.../
    
    Other informations, which you think might be helpful: FILL IT HERE
  • You should provide log directory (zipped or tarred) on some server - rapdishare.de, megaupload.com or other - because I might need it

Known bugs on Ubuntu/Debian package VMD builder

  1. Fails on other versions are probably due to paths in 1.8.7
  2. Correct it if you want - this won't be done in my release checkout function buildVMD() for more details and logs. (Probably it's something about include path to Python/NUMPY or TCL/TK in version 8.5 - try to use TCL/TK 8.4 or 8.3)
  3. VMD from this package is so sloow! It's true try to change parameter MESA to OpenGL (my laptop graphic card doesn't support OpenGL :()

Additional links about VMD

4 comments:

  1. nice! I don't know a lot about VMD, but that thing on the screenshot looks like spaghetti on LSD :D

    ReplyDelete
  2. ;) lol, it's almost spaghetti, exaclty it's protein (1A49) from PDB database - it is displayed using ribbon representation of chains :).

    ReplyDelete
  3. Hi!

    I'm a french user for the CNRS, and your installation file is very useful! I think you might add a question if user wants to add plugins in his VMD. ;D

    See ya!

    ReplyDelete
  4. To make it compatible with python2.6, I have just added the line:
    gawk '{ gsub("python2.5", "python2.6"); print }' Makefile > 1.tmp && mv 1.tmp Makefile
    when "Correcting Makefiles"

    Very useful, thanks.

    ReplyDelete