Kemutu

(paintball tournament at KOS, I-Quest Fest)

go..goo.., KEMUTU..!!=P

All out day....
Tension because 'KEMUTU' had been treated unfair...

Try our best next tym, Kemutu..!! Yahhh....(hehe..~)

Smile Practise

29 october 2009..
We learnt how to generate smile notation from molecule structures using Chemsketch. We were given 16 kind of stuctures to be drawn. It's not so easy to draw all of them because we have to follow the rules while drawing them. If the drawing has any mistake, the result, which is the smile notation, will be different. Some structures are difficult to be drawn.

After done with the drawing, we must generate smile notation for each structure. After generated all the notations, we can check all the answers at this website, http://www.daylight.com/daycgi_tutorials/smipractice.cgi , so that we know if we had done any error or mistake while drawing the structures.

PDB and Rasmol

Today class, 28th Oct 2009, we learned about Protein Data Bank (PDB).

The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards.

The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.

We must download molecule structure from PDB website, http://www.rcsb.org/
After download the 3-D molecule structure, we opened and viewed it in Rasmol.

Using Rasmol, we can display the selected molecule as wireframe, backbone, sticks, spacefill, ribbons, strands, cartoons, or molecular surface. We also can change the colour of the molecule to monochrome, CPK, shapely, group, temperature, structure, user, model or alt. Besides, we also can rotate the molecule to view each sides.

With PBD and Rasmol, now, we can easily get various kind of 3-D molecular structures and edit them according to our needs.

I found that it is kind of interesting to learn about PDB and used Rasmol software. Before this, i never heard of them. So, today's learning is very beneficial to me.

chemsketch class practical

Today, 7th of Oct, KOS class, we all were introduced to a new software, Chemsketch. I thought it's quite interesting to sketch and draw chemical structures,diagram, apparatus etc., using computer.

We were given tasks to complete sketching and drawing 5 things: energy of reaction diagram, p-orbital, d-orbital,pi-orbital,vacuum distillation apparatus, two-chain DNA strand,lipids and micelles.

We learnt to draw all of them by referring to the manual book that have been given to us.
Although we have referred to the notes, it's kind of difficult to draw the objects, since we were new to this software. Somehow, we have learnt many things, such as how to make an energy diagram and two-chain DNA strand by using polyline. We also learnt how to draw different types of orbitals by using polygon(p-orbital and d-orbital) and ellipse(pi-orbital). We drew apparatus using lab kits templates and arranged them properly according to its actual arrangement in experiment. Then, we learnt how to draw lipids and micelles using ellipse and polyline, convert it to curve then smoothen it.

After we finished our sketch, we must email our work to the lecture and post it at our blog.