SuRiZaMaNaP: October 2010

Tuesday, October 19, 2010

XML

XML TABLE

Method	Molecular Mechanics	Semi Empirical	Ab initio
Speed	Very fast speed	Fast speed	Slow speed
Accuracy	Restriction parameters	Good accuracy	Very good accuracy
Modelling	Very Good protein modelling	Good protein modelling	Best protein modelling

XML DOCUMENTATION

<Computational Method>
<Method="Molecular Mechanics">
    <Speed>Very fast speed</Speed>
    <Accuracy>Restriction parameters</Accuracy>
    <Modelling>Very Good protein modelling</Modelling>
</Method>
<Method="Semi Empirical">
    <Speed>Fast speed</Speed>
    <Accuracy>Good accuracy</Accuracy>
    <Modelling>Good protein modelling</Modelling>
</Method>
<Method="Ab initio">
    <Speed>Slow speed</Speed>
    <Accuracy>Very good accuracy</Accuracy>
    <Modelling>Best protein modelling</Modelling>
</Method>
</Computational Method>

XML TREE

Learn more about the XML at those website:

or we can discuss it in my FACEBOOK
and also my EMAIL

Tuesday, October 12, 2010

PDB (Protein Data Bank)

This is Protein Data Bank. To get this kind of picture we need to go through some process.

First,

You need to have the software called Raswin. To get software you can just simply type Raswin software in Google. Download the installer then install it.

Second,

Go to www.pdb.org to search for desired chemical structure.

Third,

Search for lexA in the pdb.

Fourth,

Download 3K22 or Crystal Structure of a LexA protein from Thermotosa maritima file.

Sixth,

Open the file in Raswin then edit it. Display it as ball & stick. Choose the colour as structure. Change the option into slab mode, hydrogens, specular, and stereo. Choose the setting pick ident and Rotate Mol.

Seventh,

After all, print scrint then paste in microsoft power point, crop it and save as picture.

Eighth,

Upload the picture into this blog.

That all..thank you so much!!!

SMILES

Learn More about SMILE from URL below
http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

From table below shows SMILES bonds

Bonds Name	Sign
SINGLE	-
DOUBLE	=
TRIPLE	#
AROMATIC	:

ACD/ChemSketch Version 8.0 for Microsoft Windows

Creating Graphical Objects

This chapter will familiarize you with the creation of graphical objects. Switch to the Draw mode before proceeding with any exercise in this chapter.
You will learn how to use Draw mode tools for creating the following objects:
• A diagram of the energy of reaction
• Various types of orbitals
• Vacuum distillation apparatus
• A two-chain DNA strand
• Lipids and micelles

Name of Object	The Picture Should Look Like
A diagram of the energy of reaction
Various types of orbitals
Vacuum distillation apparatus
A two-chain DNA strand
Lipids and micelles

All the picture below are the drawing result in ACD/Chemsketch

A diagram of the energy of reaction

Various types of orbitals

Vacuum distillation apparatus

A two-chain DNA strand

Lipids and micelles

Learn more about the chemsketch at those website:

or we can discuss it in my Facebook
and also my E-mail

SCATTER PLOT IN EXCEL

Part 1 - Beer's Law Scatter Plot and Linear Regression
Beer's Law Graph

Conc.(M)	Absorbance
0.00E+00	0.0000
4.00E-05	0.0958
8.00E-05	0.1820
1.20E-04	0.2760
1.60E-04	0.3430
2.00E-04	0.4130

unknown 1	0.1370	6.07655E-05
unknown 2	0.3650	0.000170809

Part 2 - Titration Data Plotting

Titration

Chart Axis Scale have been modified

Tittration of 50mL of 0.1M HCL

NaOH added (mL)	pH
0.00	1.00
10.00	1.17
25.00	1.48
45.00	2.28
49.50	3.30
49.75	3.60
50.00	7.00
50.25	10.40
55.00	11.68
60.00	11.96

KOS1110 – COMPUTER IN SCIENCE

TUTORIAL ON EXCEL

Finding the line of best fit

Temperature (in °C)	8	22	15	13	12	21	20	9
Percentage injured p	4.7	12.3	6.5	5.9	6.6	10.3	8.4	4.0

percentage of runners that would be injured at 27°C					13.174
temperature in which 10% of the runners were injured.					20.48255

2.Quadratic regression

Year (x)	1990	1991	1992	1993	1994	1995	1996	1997
Housing starts (y)	1193	1014	1200	1288	1457	1354	1477	1474

number of new housing starts in 2001

-404405351

For further reading about the scatter plot please go those website