SMiLES....

On the 29th of October,we had learnt about smile notation in class..

SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. it is like simplification of the writen of molecular structures.  

 After that, Mdm linda gave us assignment on smile. We were given 16 stucture of organic molecules and are asked to find their smile notation.. So in order to draw these structure wu must used the chemsketch software. After draw the structure, we can find the smile notation of the structure by clicking 'tools' , 'generate' , 'smile notation'.. 

However. not all these structure are drawn correctly, we need to check if the notation given are correct. these notation can be checked through http://www.daylight.com/daycgi_tutorials/smipractice.cgi. These stucture cannot be simply drawn as the drawing must follow the rules in drawing the organic molecules.

This is the page of the website that mentioned at the above.

 then we checked the answers by writing the notation in the smiles box..

This is the structure and the smiles notation that we had been assingned to do.

 

 

This was the last assignment for this subject. And now we are going to have our final examination for this semester. I hope that all of us can answers the exams smoothly and gets results with flying colours.

Last but not least...

Thank you Mdm Linda for giving us knowledge and helping us in class.

And also not to forget thanks for ur care..

:-)

PDB- Protein Data Bank

wHAT IS pdb??

PDB stand for protein database. It is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids.The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, can be accessed at no charge on the internet. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.The PDB is a key resource in areas of structural biology, such as structural genomics.

We are also being told the website about the PDB which is http://www.rcsb.org/pdb/home/home.do

The website is the PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. It is a resource for studying biological macromolecules.

In the class we have been taught to use the raswin / the rasmol  software to viewing and editing the structure molecules. we use trypsin molecules that we downloads in the website that i refer at the above. 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.We are assigned to use 2 types of trypsin molecules.

This are the two type of trypsin molecules

 

 

chemsketch........ 7 okt 2009

In our next kos1110 class,we learn to use new application. We use chemsketch software too sketch organic compound structure.

First, before doing the assignment mdm linda asked us to do exercise in sketching the structure of the organic compound. It quite difficult at first,but eventually i understand how to do it. After about practicing about an hour, we were given task to be completed.
 we need to sketch and draw chemical structures,diagram, apparatus etc., usingthe chemsketch software.

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.However, it is quite 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.

This the structure that we had been asked to do..

 

 \