stand alone | pyMOL plugin | examples for stand alone | examples for pyMOL plugin

Version 0.99.4 - Beta Release 2006-Apr-20

Unix/Linux source code (gcc version 3.4.3): caver_unix_v0.99.4.tar.gz

Patches: patch-0.99.4-001

How to apply a patch on linux/unix:

cp patch-name  caver_unix_v<VERSION>
patch -p1 < patch-name

Linux Binary: caver_unix_v0.99.4binary.tar.gz

PYMOL plugin version 0.99.4

Unix/Linux: caverPLUG_unix_v0.99.4.tar.gz

• pre-clustering of found tunnels

Version 0.99.2 - Beta Release 2006-Jan-02

Unix/Linux source code (gcc version 3.4.3): caver_unix_v0.99.2.tar.gz

Linux Binary: caver_unix_v0.99.2binary.tar.gz

Widows source code (Microsoft Visual C++): caver_win_v0.99.2.zip

Windows Binary: caver_win_v0.99.2binary.zip

Windows Installation Package: caverall.msi

• caver binary
• qconvex program
• plugin (caver.py) that can be installed into Pymol
• examples

• finds n most probable tunnels, see manual
• output files are in single directory
• pdb2caver converter

Version 0.99.1 - Beta Release 2005-Sep-22

Unix/Linux source code (gcc version 3.4.3): caver_unix_v0.99.1.tar.gz

Linux Binary: caver_unix_v0.99.1binary.tar.gz

Widows source code (Microsoft Visual C++): caver_win_v0.99.1.zip

Windows Binary: caver_win_v0.99.1binary.zip

• CAVER tests that qhull is present
• better input error checking

Version 0.99 - Release 11. Aug. 2005

Unix/Linux source code (gcc version 3.4.3): caver_unix_v0.99.tar.gz

Linux Binary: caver_unix_v0.99binary.tar.gz

Widows source code (Microsoft Visual C++): caver_win_v0.99.zip

Windows Binary: caver_win_v0.99binary.zip

Installation of binary version:

CAVER uses 'qconvex' routine from Qhull program package. This package should be installed first before running CAVER!
Download and install your-platform version of Qhull program from http://www.qhull.org/download

• On Linux:
  1. Download file caver_unix_v<VERSION>binary.tar.gz
  2. Extract the file

  tar xfvz caver_unix_v<VERSION>binary.tar.gz
  cd caver_unix_v<VERSION>binary
  

  3. Install program

  ./install --prefix <installation directory>       (default /usr/local/share/CAVER)
  

  4. Set PATH variable

  export PATH=$PATH:<installation directory>           
  export PATH=$PATH:<qhull binaries directory>         (for bash-shell)
  

• On Windows:
1. Download installation package caver_win_v<VERSION>binary.zip
2. Use some extraction program such as Total Commander with appropriate plugin.
3. Copy extracted files into "C:\CAVER"
4. Add CAVER directory to the PATH (System variable):
   Choose Settings->Control Panel->System->Advanced tab
   Add "C:\CAVER" to the right end of the "PATH" in the User Variables.
   Add Qhull binary directory (usually "C:\Program Files\qhull-2003.1") to the "PATH" variable
   Click "Set", "OK" or "Apply"

Compilation of source codes:

CAVER uses 'qconvex' routine from Qhull program package. This package should be installed first before running CAVER!
Download and install your-platform version of Qhull program http://www.qhull.org/download

• On Linux:
  1. Download file caver_unix_v<VERSION>.tar.gz
  2. Install program
  If you are root:

  tar xfvz caver_unix_v<VERSION>.tar.gz
  cd caver_unix_v<VERSION>binary/
  ./configure
  make
  make install
  

  If you are a normal user install program to some directory (/home/username/CAVER)

  tar xfvz caver_unix_v<VERSION>.tar.gz
  cd caver_unix_v<VERSION>binary/
  ./configure --prefix=/home/username/CAVER
  make
  make install
  export PATH=$PATH:/home/username/CAVER
  export PATH=$PATH:<qhull binaries directory>         (for bash-shell)
  

• On Windows:
1. Download file caver_win_v<VERSION>.zip
2. Use some extraction program such as Total Commander with appropriate plugin.
3. Copy extracted files into "C:\development\CAVER" or where ever you want.
4. Open project Caver.dsw in Microsoft Visual C++
   
5. Build the project
   
6. Copy the binary (caver.exe) to some directory (let's say "C:\Program Files\CAVER")
   
7. Add CAVER directory to the PATH:
   Choose Settings->Control Panel->System->Advanced tab
   Add "C:\Program Files\CAVER" to the right end of the "Path" in the User Variables.
   Add Qhull binary directory (usually "C:\Program Files\qhull-2003.1") to the "Path" variable
   Click "Set", "OK" or "Apply"

Download Caver PyMOL Plugin Version 1.0

Expected version of PyMOL should be higher than 0.97 (and used Python higher than 2.2.2.)
Actual version of PyMOL can be downloaded at http://pymol.sourceforge.net.

Installation of CAVER plugin:

1. Install Qhull and CAVER to your system (see above instructions)
2. Check python version used by pyMOL. It needs to be higher then 2.2.2 (type 'print sys.version;' in pyMOL command line)
3. For Linux:
4. Download plugin
   • pymolplug.tar.gz (version 0.99)
   • caverPLUG_unix_v0.99.2.tar.gz (Beta 0.99.2 - cooperates with CAVER 0.99.2, enables to find more tunnels)
5. Extract file

   tar xfvz pymolplug.tar.gz

6. Plugin suppose CAVER installation in /usr/local/share/CAVER/bin/caver, if not, please edit the file 'caver.py' and change the line with CAVER_BINARY_LOCATION to appropriate CAVER location.
7. For Windows:
8. Download plugin
   • pymolplugwin.tar.gz (version 0.99)
   • caverPLUG_win_v0.99.2.zip (Beta 0.99.2 - cooperates with CAVER 0.99.2, enables to find more tunnels)
9. Extract file by some extraction program such as Total Commander with appropriate plugin
10. Plugin suppose CAVER installation in C:\CAVER\caver.exe, if not, please edit the file 'caver.py' and change the line with CAVER_BINARY_LOCATION to appropriate CAVER location.
11. Install plugin (select 'Install Plugin' in PyMOL->menu->Plugin and open file caver.py)
    
    • On Linux you should have root privileges to install plugins in PyMOL (use "su", call "pymol" (sometimes you should disable display access control "xhost +", after installation type "xhost -"), install plugin)
    
    examples for pyMol plug-in