rasmol uses patched wrapper instead of patching the source code
|Deletions are marked like this.||Additions are marked like this.|
|Line 30:||Line 30:|
|You can run ASE without RasMol, you just won't be able to plot atoms with the RasMol plotter.||You can run ASE without RasMol, you just won't be able to plot atoms with the *RasMol* plotter.|
|Line 32:||Line 32:|
|The `binary rpm`_ can be used for installing Rasmol on RHEL5 or FC6,||The `binary rpm`_ can be used for installing *RasMol* on RHEL5 or FC6,|
|Line 35:||Line 35:|
|to run *Rasmol* on remote displays (see below). Alternatively the source code of *Rasmol*||to run *RasMol* on remote displays (see below). Alternatively the source code of *RasMol*|
Download and install ASE
The following packages are required for basic ASE functionality:
- Python 2.2 or later is required. Python is available from http://www.python.org.
Numeric Python. Use the latest version 24.2.
Build preferably from our python-numeric-24.2-1.1.el5.fys.src.rpm or edit customize.py file to configure Numeric Python to use the system lapack library.
- Scientific Python from http://dirac.cnrs-orleans.fr/ScientificPython/. Use the 2.4.11 version.
The following packages are optional, since they enable the use of some specific external tools. You only need to install these tools if you want to use the extra tools mentioned:
Rasmol from http://www.openrasmol.org/.
You can run ASE without RasMol, you just won't be able to plot atoms with the RasMol plotter.
The rasmol-2.7.3-2.1.el5.fys.i386.rpm can be used for installing RasMol on RHEL5 or FC6, for older versions build from rasmol-2.7.3-2.1.el5.fys.src.rpm. Our (S)RPMS use a python wrapper (see http://bioinformatics.org/pipermail/molvis-list/2005q2/000173.html), which allows to run RasMol on remote displays (see below). Alternatively the source code of RasMol could be patched (see http://lists.centos.org/pipermail/centos/2006-February/060793.html). For those who prefer to patch the source, it is included in rasmol-2.7.3-2.1.el5.fys.src.rpm, but requires uncommenting the corresponding line in the spec file.
A trick for running Rasmol on remote displays. Check out your X-Windows DISPLAY variable:# echo $DISPLAY localhost:11.0
then replace localhost with 127.0.0.1:# setenv DISPLAY 127.0.0.1:11.0
(Be sure that the number after the : is the same as before!). Then Rasmol works!
Why does this work? Rasmol recognize the localhost in the $DISPLAY variable and then it uses a faster way to update the display, but one that only works locally - it is fooled by ssh forwarding the apparently local display to the remote machine you are sitting at. 127.0.0.1 is the IP number of localhost, but Rasmol does not recognize that.
- Gnuplot. ASE can use Gnuplot via the Gnuplot-Python interface from http://sourceforge.net/projects/gnuplot-py/. At CAMP/Niflheim we call this RPM python-gnuplot. Use the 1.7 version.
Python Pexpect from http://pexpect.sourceforge.net/.
The current version of Pexpect is 2.1, but at Niflheim we use an old version 0.999. Both versions can be downloaded from the above site. At CAMP/Niflheim we install the Pexpect RPM under the name of python-pexpect.
RPM packages for Pexpect can be found on rpmfind.
- Matplotlib http://matplotlib.sourceforge.net/. Use the 0.90.0 version.
vtk http://www.vtk.org/. After installation you may need (if libvtkRenderingPythonTkWidgets.so is missing) to make a link:
ln -s /usr/lib/libvtkRenderingPythonTkWidgets.so.5.0 /usr/lib/libvtkRenderingPythonTkWidgets.so
and set the path manually:
Use the 5.0.3 version.
A Python-based package such as ASE or any of the above mentioned extra packages are usually downloaded as a tar-ball or from a CVS repository.
In order to install the package you have two options (both require superuser priviledges):
Install as a Python package:
python setup.py install
Build an RPM package and install it on one or many machines:
python setup.py bdist_rpm
You have to locate the finished RPM package after building, it may be in the dist/ subdirectory if correctly implemented, or in another directory such as build/bdist.linux-x86_64/rpm/RPMS/ (for the x86_64 architecture).
If you don't have root permissions, you will need to add the package directory to your PYTHONPATH environment variable and use your local copy of the code.
Make sure that everything works by running the test suite:
cd ASE/Tests python test.py
To get started with Campos ASE, point your browser at the CamposASE homepage.