Linux


Administrative privileges are NOT needed to install the Linux binary distribution of Open3DALIGN.

If you wish to determine the most appropriate version for your system, download choose_version (a small utility based on Dave Jones' x86info), open a terminal, move to the folder where you downloaded choose_version and type:

$ chmod +x choose_version
$ ./choose_version


Then, download to your preferred location the .bin installer matching your system. Run the latter by issuing the following commands:

$ chmod +x your_open3dalign_version_setup.bin
$ ./your_open3dalign_version_setup.bin


Inside the open3dtools folder you will find a bin folder containing the open3dalign.sh wrapper script, which calls the open3dalign executable after properly setting the LD_LIBRARY_PATH, plus a few TINKER executables and libraries.
In fact, the open3dalign executable has been built with Oracle Solaris Studio Compiler for Linux version 12 update 3 and linked with the Sun Performance Library. The Linux distribution of this compiler does not allow for full static linking of libraries, so the LD_LIBRARY_PATH has to be properly set in order for the OS to find the dynamic link library needed by Open3DALIGN, namely libmtsk.so.1. If you invoke Open3DALIGN using the wrapper script open3dalign.sh included in the bin directory, LD_LIBRARY_PATH will be automatically set for you.

Instead, in the open3dalign folder you will find a README file, the license, the ChangeLog and a copy of the documentation.

Open3DALIGN depends on OpenBabel for file format conversions and atom type assignment, and on Pharao for molecular alignment.

Unless you already have the latest version of openbabel_for_open3dtools installed on your system, you will want to download also the openbabel_for_open3dtools_linux_setup.bin installer which includes all necessary dependencies for Open3DALIGN, and install it in the same place where you previously installed Open3DALIGN. Should you at a later stage decide to download and install another tool of ours which has the same dependency from OpenBabel, such as Open3DGRID or Open3DQSAR, just install it in the same place where you previously installed Open3DALIGN and openbabel_for_open3dtools, and everything will work out of the box as long as you keep the original arrangement of the directory tree.

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Last update:
May 31. 2015 20:39:55

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Would you like to test your
alignment in a 3D-QSAR
model? Try Open3DQSAR
Just wish to compute a MIF?
Try Open3DGRID