Demos and Tutorials
1. Boot the computer with VigyaanCD
2. Click the Vigyaan Demos icon (the green V icon) on the desktop. Required files will be copied in the home directory and an interactive shell will start.
3. change current directory:
>cd ~/Vigyaan4. There are 12 demos (each in separate directory): Artemis, ClustalX, Ghemical, GROMACS, Jmol, NJPlot, OpenBabel, PSI3, PyMOL, Rasmol, Raster3D and TINKER. You can cd each directory and type demo. For example:
>cd ClustalXDemo description:
ClustalX, Sequence alignment demo: This demo calls clustalx with a filename as argument. The filename is PPIases, which contains sequence of 10 proteins in FASTA format. To perform sequence alignment from top menu select: Alignment -> Do Complete Alignment. On the pop-up box click on ALIGN.
Ghemical, MD demo (small molecule): This demo loads a previous MM project (molecular mechanics project) from file sample.mm1gp. To add hydrogens click mouse right button on black area and from the pop-up menu select:Build -> Hydrogens -> Add. To optimize the structure from the pop-menu select: Compute -> Geometry Optimization. Click OK. To perform molecular dynamics: Compute -> Molecular Dynamics.
GROMACS, MD demo (peptide in water): This demo prepares and performs molecular dynamics for a peptide in water. When prompted press Enter and follow instructions on screen.
Jmol, Quantum chemistry calculation visualization demo: This demo loads an output file from GAMESS-US run (Hessian calculation for proton between 2 water molecules). Use Extras -> Vibrate to view different normal modes.
Open Babel, Structure file format conversion demo: This demo converts a protein structure from PDB format to XYZ format using command babel.
NJPlot, Phylogenetic tree creation demo: This demo create a phylogenetic tree based on a sample input file.
PSI3, Quantum chemistry calculation demo: This demo runs a quantum chemistry calculation using PSI3 package. The calculation performed is SCF optimization of CH4 with DZP basis set.
PyMOL, Structure visualization and high-quality image rendering demo: This demo loads a sample project with a protein and 3 conformations of a peptide in the active-site. To change the display use options from S (show), H (hide), L (label) and color menu. To render a high-quality image use ray option in the main menu. To save image use from main menu: File -> Save Image.
Rasmol, Structure visualization demo: This demo loads a protein for visualization. You can use mouse to rotate the molecule. Display and colors can be changed from top menu.
Raster3D, High quality image rendering (for biomolecules) demo: This demo creates a high quality image of a protein active-site.
TINKER, Molecular modeling demo: This demo creates a TINKER file from PDB file for a protein, performs a single point energy calculation and computes molecular volume and surface area.
EMBOSS:Online and on VigyaanCD:
GROMACS:Online and on VigyaanCD:
/usr/local/share/Raster3D/examples/README.examples (README as text file)
/usr/local/share/tinker/example/README (README as text file)
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