Demos and Tutorials

>cd ~/Vigyaan

>cd ClustalX
>./demo

Artemis, Genome viewer demo: This demo loads a genome for viewing. In this demo a local copy of genome is loaded, however Artemis can also load sequences from the Internet.

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.