CHEMSKETCH

What is CHEMSKETCH???

ChemSketch is a chemical structure drawing program developed by ACD/Labs. It is a free download for educational use. It can be used to produce structures of organic molecules, names of organic molecules as well as Lewis structures, 3D structures, space filling models or ball and stick models, among other things. 

WHAT IT CAN DO???

Among other features, ChemSketch has the ability to:

• Draw and view structures in 2D, or render in 3D to view from any angle
• Draw reactions and reaction schemes, and calculate reactant quantities
• Generate structures from InChI and SMILES strings
• Generate IUPAC systematic names for molecules of up to 50 atoms and 3 ring structures
• Predict logP for individual structures
• Search for structures in the built-in dictionary of over 165,000 systematic, trivial, and trade names

GETTING STARTED......

First and for most, go to  http://www.acdlabs.com/products/draw_nom/draw/chemsketch/ and download the ChemSketch. Install the software and you can start trying to make some sketching.

   For the beginning,you need to know some basics of ACD/ChemSketch :

     

Once ACD/ChemSketch has been installed on your computer, follow these basic steps to start it:

1. Start Windows.

2. Double click on the ACD/ChemSketch icon to start ACD/ChemSketch.

OR choose the ACD/ChemSketch icon from the Start/Run menu in the Windows 95 or NT

Taskbar

OR double click on the program file “chemsk.exe” in the ACD folder.

3. You will see the splash screen appear, followed by the ChemSketch window:

4. If this is the freeware version, you will see a 15-second list of ACD products scroll by. Be

patient and click Cancel when it becomes active.

5. Then you will see a Tip of the Day box, which you can close after reading.

 Structure and Draw Mode

When ACD/ChemSketch starts up, you will find many menu commands and toolbar buttons

dimmed (inactive). They will be enabled as soon as you draw a structure.

In the ChemSketch Window, there are two modes, Structure and Draw. You switch between

them using the buttons in the upper left-hand corner:

In the Structure Mode you draw structures and reaction schemes while the Draw Mode presents

you with the tools for entering text and drawing various graphical objects.

Structure Mode Screen

Below you can see the screen with the Structure Mode enabled. Please pay attention to the

names and position of the toolbars, since we are going to use these terms throughout the whole

Guide.

Title bar shows the name of the program and the name of the currently open file. The default file

name is NONAMExx.SK2, where ‘xx’ is a counter.

Menu bar contains a series of words. Each word links to a list (‘menu’) of related commands for

working in the ChemSketch window in Structure mode.

General toolbar located right below the menu bar includes tools that are present in both Structure and Draw modes and will help you with tasks relevant to both modes such as: saving, opening files, undoing/redoing operations, copying and pasting, zooming in and out, as well as inserting various templates.

Structure toolbar placed below the General toolbar and only present in the Structure mode. This

contains tools for drawing and manipulating chemical structures, as well as buttons that link you to additional modules.

Atoms toolbar displayed vertically to the left of the screen contains buttons representing atoms,

as well as tools for changing atom properties (charge, valence, numbering, etc.).

Reference toolbar placed to the right of the window contains the Table of Radicals and various

buttons representing ready-made radicals you take from the table. You can also access

ACD/Dictionary from this toolbar.

Workspace is the open area in the middle where structures are drawn. (Sample shown.)

Color Palette at the bottom of the workspace allows you to quickly color atoms and bonds in the

selected chemical structures (by clicking or right-clicking on the colors).

Status bar contains information that may be useful for the current moment: name of the SK2 file

you are working on, page number in the SK2 file, number of fragments in the workspace,

molecular formula of the selected structure, as well as one of the available chemical properties for the selected structure. It also contains a button for automatic I-Lab access.

Draw Mode Screen

Below you can see the screen with the Draw Mode enabled. Please, pay attention to the names

and position of the toolbars, since we are going to use these terms throughout the whole guide.

Title bar shows the name of the program and the name of the currently open file. The default file

name is NONAMExx.SK2, where ‘xx’ is a counter.

Menu bar contains a series of words. Each word links to a list (‘menu’) of related commands for

working in the ChemSketch window in Draw mode.

General toolbar located right below the menu bar includes tools that are present in both Structure and Draw modes and will help you with tasks general for both modes such as, saving, opening files, undoing/redoing operations, copying and pasting, zooming in and out, as well as inserting various templates.

Editing toolbar placed below the General toolbar and only present in the Draw mode

incorporates tools for editing and manipulating drawn graphical objects.

Drawing toolbar displayed vertically to the left of the screen contains buttons for drawing various graphical objects and text.

Workspace is the open area in the middle where graphical objects are drawn and text is typed.

Color Palette at the bottom of the workspace allows you to quickly color selected objects (by

clicking or right-clicking on the colors).

Status bar contains information that may be useful for the current moment: name of the file you

are working on, status of the document and page number.

SO, those are the most basics thing you need to know...as it is quiet long to explain everything,i think you may visit THIS link by your own to know more about how to use this ChemSketch. Good luck exploring it n enjoy!!!

LET'S PURIFY OUR HEART!!
	AL-MATHURAT	DHUHA	QURAN RECITATION	CONGREGATIONAL PRAY
MONDAY
TUESDAY
WEDNESDAY
THURSDAY
FRIDAY
SATURDAY
SUNDAY

-eXtensible Markup Language-

  -designed to transport and store data-

-a markup language much like HTML-

-tags are not predefined. You must define your own tags-

-is designed to be self-descriptive-

The Difference Between XML and HTML

XML	HTML
was designed to transport and store data, with focus on what data is	was designed to display data, with focus on how data looks

XML Does Not DO Anything

Maybe it is a little hard to understand, but XML does not DO anything. XML was created to structure, store, and transport information.

The following example is a note to Tove, from Jani, stored as XML:

<note>

<to>Tove</to>

<from>Jani</from>

<heading>Reminder</heading>

<body>Don't forget me this weekend!</body>

</note>

The note above is quite self descriptive. It has sender and receiver information, it also has a heading and a message body.

But still, this XML document does not DO anything. It is just information wrapped in tags. Someone must write a piece of software to send, receive or display it.

With XML You Invent Your Own Tags

The tags in the example above (like <to> and <from>) are not defined in any XML standard. These tags are "invented" by the author of the XML document.

That is because the XML language has no predefined tags.

The tags used in HTML are predefined. HTML documents can only use tags defined in the HTML standard (like <p>, <h1>, etc.).

XML allows the author to define his/her own tags and his/her own document structure.

XML is Not a Replacement for HTML

XML is a complement to HTML.

It is important to understand that XML is not a replacement for HTML. In most web applications, XML is used to transport data, while HTML is used to format and display the data.

My best description of XML is this:

XML is a software- and hardware-independent tool for carrying information.

So?? still confused after such a long explanation.

.

do visit www.w3schools.com/xml/‎ for further & better explanation. or u can just type in XML @ any search engine such as yahoo.com, google.com and many more.

SMILES!!!

 it is not just an expression..actually, almost none of us knew that this term could refer to other meaning.

SO, WHAT IS SMILES??

Simplified Molecular-Input Line-Entry System 

ITS FUNCTION??

• describing the structure of chemical molecules using short ASCII strings in the form of line notation 
• SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensionalmodels of the molecules.

ITS FOUNDER??

 David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth (1980).

ASSISTS BY??

• Gilman Veith and Rose Russo (USEPA) and Albert Leo and Corwin Hansch (Pomona College)
•  Arthur Weininger (Pomona; Daylight CIS) and Jeremy Scofield (Cedar River Software, Renton, WA) for assistance in programming the system

PROJECT'S FUNDER??

The Environmental Protection Agency

MODIFIED BY??

•  Daylight Chemical Information Systems Inc
•  Blue Obelisk (2007) - "OpenSMILES"
•  Wiswesser Line Notation (WLN)
•  ROSDAL
• SLN (Tripos Inc)
• IUPAC - InChI

here some example of SMILES notation ;

SMILES	NAME
CC	ethane
O=C=O	carbon dioxide
C#N	hydrogen cyanide
CCN(CC)CC	triethylamine
CC(=O)O	acetid acid
C1CCCCC1	cyclohexane
c1ccccc1	benzene

SMILES Specification Rules

SMILES notation consists of a series of characters containing no spaces. Hydrogen atoms may be omitted (hydrogen-suppressed graphs) or included (hydrogen-complete graphs). Aromatic structures may be specified directly or in Kekulé form.

There are five generic SMILES encoding rules, corresponding to specification of atoms, bonds, branches, ring closures, and disconnections.

3.2.1 Atoms

Atoms are represented by their atomic symbols: this is the only required use of letters in SMILES. Each non-hydrogen atom is specified independently by its atomic symbol enclosed in square brackets, [ ]. The second letter of two-character symbols must be entered in lower case. Elements in the "organic subset" B, C, N, O, P, S, F, Cl, Br, and I may be written without brackets if the number of attached hydrogens conforms to the lowest normal valence consistent with explicit bonds. "Lowest normal valences" are B (3), C (4), N (3,5), O (2), P (3,5), S (2,4,6), and 1 for the halogens. Atoms in aromatic rings are specified by lower case letters, e.g., aliphatic carbon is represented by the capital letter C, aromatic carbon by lower case c. Since attached hydrogens are implied in the absence of brackets, the following atomic symbols are valid SMILES notations.

C	methane	(CH4)
P	phosphine	(PH3)
N	ammonia	(NH3)
S	hydrogen sulfide	(H2S)
O	water	(H2O)
Cl	hydrochloric acid	(HCl)

Atoms with valences other than "normal" and elements not in the "organic subset" must be described in brackets.

[S]	elemental sulfur
[Au]	elemental gold

Within brackets, any attached hydrogens and formal charges must always be specified. The number of attached hydrogens is shown by the symbol H followed by an optional digit. Similarly, a formal charge is shown by one of the symbols + or -, followed by an optional digit. If unspecified, the number of attached hydrogens and charge are assumed to be zero for an atom inside brackets. Constructions of the form [Fe+++] are synonymous with the form [Fe+3]. Examples are:

[H+]	proton
[Fe+2]	iron (II) cation
[OH-]	hydroxyl anion
[Fe++]	iron (II) cation
[OH3+]	hydronium cation
[NH4+]	ammonium cation

3.2.2 Bonds

Single, double, triple, and aromatic bonds are represented by the symbols -, =, #, and :, respectively. Adjacent atoms are assumed to be connected to each other by a single or aromatic bond (single and aromatic bonds may always be omitted). Examples are:

CC	ethane	(CH3CH3)
C=O	formaldehyde	(CH2O)
C=C	ethene	(CH2=CH2)
O=C=O	carbon dioxide	(CO2)
COC	dimethyl ether	(CH3OCH3)
C#N	hydrogen cyanide	(HCN)
CCO	ethanol	(CH3CH2OH)
[H][H]	molecular hydrogen	(H2)

For linear structures, SMILES notation corresponds to conventional diagrammatic notation except that hydrogens and single bonds are generally omitted. For example, 6-hydroxy-1,4-hexadiene can be represented by many equally valid SMILES, including the following three:

Structure	Valid SMILES
	C=CCC=CCO
CH2=CH-CH2-CH=CH-CH2-OH	C=C-C-C=C-C-O
	OCC=CCC=C

3.2.3 Branches

Branches are specified by enclosing them in parentheses, and can be nested or stacked. In all cases, the implicit connection to a parenthesized expression (a "branch") is to the left. Examples are:

CCN(CC)CC	CC(C)C(=O)O	C=CC(CCC)C(C(C)C)CCC
Triethylamine	Isobutyric acid	3-propyl-4-isopropyl-1-heptene

3.2.4 Cyclic Structures

Cyclic structures are represented by breaking one bond in each ring. The bonds are numbered in any order, designating ring opening (or ring closure) bonds by a digit immediately following the atomic symbol at each ring closure. This leaves a connected non-cyclic graph which is written as a non-cyclic structure using the three rules described above. Cyclohexane is a typical example:

There are usually many different, but equally valid descriptions of the same structure, e.g., the following SMILES notations for 1-methyl-3-bromo-cyclohexene-1:

Many other notations may be written for the same structure, deriving from different ring closures. SMILES does not have a preferred entry on input; although (a) above may be simplest, others are just as valid.

A single atom may have more than one ring closure. This is illustrated by the structure of cubane in which two atoms have more than one ring closure:

Generation of SMILES for cubane: C12C3C4C1C5C4C3C25.

If desired, digits denoting ring closures can be reused. As an example, the digit 1 used twice in the specification:

O1CCCCC1N1CCCCC1

The ability to re-use ring closure digits makes it possible to specify structures with 10 or more rings. Structures that require more than 10 ring closures to be open at once are exceedingly rare. If necessary or desired, higher-numbered ring closures may be specified by prefacing a two-digit number with percent sign (%). For example, C2%13%24 is a carbon atom with a ring closures 2, 13, and 24 .

3.2.5 Disconnected Structures

Disconnected compounds are written as individual structures separated by a "." (period). The order in which ions or ligands are listed is arbitrary. There is no implied pairing of one charge with another, nor is it necessary to have a net zero charge. If desired, the SMILES of one ion may be imbedded within another as shown in the example of sodium phenoxide.

Matching pairs of digits following atom specifications imply that the atoms are bonded to each other. The bond may be explicit (bond symbol and/or direction preceding the ring closure digit) or implicit (a nondirectional single or aromatic bond). This is true whether or not the bond ends up as part of a ring.

Adjacent atoms separated by dot (.) implies that the atoms are not bonded to each other. This is true whether or not the atoms are in the same connected component.

For example, C1.C1 specifies the same molecule as CC(ethane)

if SMILES manage to draw your attention, do click this to know more.

Protein Data Bank (PDB)

Assalamualaikum...today i'm gonna tell you about protein data bank.
i know what comes first in your mind when you read the title..you must be like.."What is that?", "Oh...there is bank for proteins..","Really?Bank for proteins?"..and those kind of questions pop up in your head,right?(no?err...)..what is this thing actually?..what can i say about PDB is that PDB is a cloud storage to store all the data about proteins..so,let's find out more about this PDB!!

WHAT IS PDB?

 The PDB is a single worlwide repository for 3D structural data of biological molecules. It is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, bibliographic citations, primary and secondary structure, information, and crystallographic structure factors and NMR experimental data. It also includes proteins, nucleic acids and viruses.

Moreover,the PDB archive is available at no cost to users. The PDB has an international community of users, including biologists (in fields such as structural biology, biochemistry, genetics, pharmacology); other scientists (in fields such as bioinformatics, software developers for data analysis and visualization); students and educators (all levels); media writers, illustrators, textbook authors; and the general public.
to learn more about this PDB things, visit  http://www.rcsb.org/pdb/home/home.do

I did found some of interesting protein structures when i went through the website. Most of us only know about protein superficially. These are the common ones :

Type of proteins	Functions
Enzymes	Reaction catalysis
Muscles	Structural proteins
Antibodies	Defense proteins
Hormones	Regulatory proteins

However, there are more than that. In the website,you can find all the data including structures and information regarding to protein..Here are some of it :
P.S: click on the link provided for further info


1) Amylase

CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 

ALPHA-AMYLASE 2 MUTANT F286A  

 http://www.rcsb.org/pdb/explore/explore.do?structureId=1JF5

2) HtrA

HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues  

http://www.rcsb.org/pdb/explore/explore.do?structureId=3MH4


3) Lexa

LEXA S119A MUTANT 

 http://www.rcsb.org/pdb/explore/explore.do?structureId=1JHH

4) pepsin

REVISED 2.3 ANGSTROMS STRUCTURE OF PORCINE PEPSIN. EVIDENCE FOR A FLEXIBLE SUBDOMAIN   

http://www.rcsb.org/pdb/explore/explore.do?structureId=3PEP


5) Trypsin

STRUCTURAL EFFECTS INDUCED BY REMOVAL OF A DISULFIDE BRIDGE. THE

X-RAY STRUCTURE OF THE C30A(SLASH)C51A MUTANT OF BASIC

PANCREATIC TRYPSIN INHIBITOR AT 1.6 ANGSTROMS 

http://www.rcsb.org/pdb/explore/explore.do?structureId=7PTI

so..what are you waiting for?? explore PDB if you wanna know more about other structures. Currently there are more than 90 000 structures have been deposited @ the PDB.. that's it for today..arios amigos!