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The Secret Path -

The Secret Path -

The Secret Path

With the same look-and-feel as ISIS/Draw, Accelrys Draw delivers speed and efficiency to your chemical drawing experience.

Why upgrade from what you're already using?

  • Improved creation and presentation of chemical structures, biologics and chemical aspects of biologics
  • Additional features such as multiple undo, name-to-structure, structure-to-name conversion, molecule templates, ChemDraw file support, InChI and Canonical SMILES support
  • An all-purpose drawing tool that enables fast and easy structure and reaction drawing
  • Easy-to-use Rgroup functionality
  • Multiple free add-ins to support desk top searching, file viewing, reaction stoichiometry calculations, calculate as you draw physicochemical properties, Markush structure enumeration, ACD lab integration and much more...

Accelrys Draw can easily swap out existing ISIS/Draw or ChemDraw applications.

 

The Secret Path -

Click here for more details about Rgroups, an example, and a detailed procedure how to draw a Markush query.

To draw a Markush query:

  1. Draw the root structure. Use the other drawing tools.

  2. Add Rgroup atom to the root structure.

    1. Click the "Create Markush structure or query"v tool.
    2. Click the atom that you want to replace.
    3. Select an Rgroup from the palette.

  3. Draw the Rgroup members with the chemical drawing tools. Step 4 will always add an additional bond. Remove the CN bond of teh default NO2 query.

  4. Add Rgroup members.

    1. Click the "Create Markush structure or query" tool.
    2. Click the fragment that you want to add.
    3. Drag and drop the fragment onto the Rgroup definition (Rn=). Try toselect the whole group. Wait until you have a blue boy around the group.

  5. (Optional) Move attachment points.

    1. Click the Markush Query tool.
    2. Click the asterisk of the attachment point.
    3. Drag and drop the asterisk onto the atom that you want.
  6. (Optional) Change the occurence. If an Rgroup atom appears at more than one instance (or place) in the root structure, you see "R1 = n (where n is defined as the number of occurences), R2 >0, etc." appear automatically next to the Rgroup definition (Rn =). For each such Rgroup, you need to specify the frequency (occurrence), the number of times that a member of this Rgroup must appear in retrieved structures. To change the frequency:
    1. Select the Rgroup Query Tool.
    2. Click the occurence definition (R1 = n), located next to the Rgroup definition (Rn =).
    3. Select a number from the dialog box that is displayed.
    4. Click OK to accept your selection. The frequency definition is updated with your selection.

 

The Secret Path

  
Generic  Structure Enumerator

The enumerator works against structures defined using the Rgroup tool in Accelrys Draw. In this mode you specify a scaffold with a number of Rgroup labels, then to add fragments to the Rgroup identifiers. The Add-in will calculate the complete set of structures that the Rgroups define.

You can also define a generic region using the Sgroup tool. Draw the basic structure and using the Sgroup tool, drag a pair of brackets around a region that is repeated in the substance. From the dropdown select generic for the bracket type, then select apply and exit from the dialog. Right click on one of the brackets and select the Attach Data option. In the dialog enter REPEATRANGE into the Field description box, and then enter the range in the Data box; leave the Search Operator set to none; the Tag field is optional. A contiguous range is required in the Data box, for example 3-6.

A structure can contain both Rgroup definitions and Sgroup definitions, but they cannot overlap or be nested.

You have the option to enumerate on to Accelrys Draws canvas, into an SDfile, or into an Isentris for Excel compatible spreadsheet.
 		 The Secret Path  

The Secret Path -

To the untrained eye, it is just a gap in the trees—a scar of dirt and moss leading into a damp, green twilight. But to those who walk it, The Secret Path is a time machine, a confessional, and a sanctuary all rolled into one. The path begins with a lie: a sign nailed to a rotting post that reads "Dead End." Step past it, and the volume of the world changes. The whine of traffic dissolves into the crunch of fallen chestnuts. The manicured lawns give way to wild blackberry brambles that snag your sleeves like a grandmother trying to keep you for dinner.

And you realize that the secret isn't the path itself. The secret is that beauty still exists in the margins. Peace still hides in the overgrown lots. And adventure is never more than a turn away from the ordinary. The Secret Path

“You can’t put a price on a place that holds your memories,” says a young father pushing a stroller down the trail. He stops to point out a knothole in an oak tree to his daughter. “See that? Your uncle jammed a G.I. Joe in there in 1998. Looks like he’s still there.” The path ends abruptly at a chain-link fence overlooking a retention pond and the rear of a big-box store. It is an ugly, utilitarian view. But if you turn around, you see the tunnel of gold and green you just walked through. To the untrained eye, it is just a

 		 http://accelrys.com/products/informatics/cheminformatics/draw/add-ins.html  

Chemical Drawing Programs The Comparison of Accelrys (Accelrys) Draw, ChemDraw, DrawIt, ACD/ChemSketch and Chemistry 4-D Draw

Dr. Tamas E. Gunda

University of Debrecen, POB 70, H-4010 Debrecen, Hungary, e-mail:

Last major update : 1.11.2011

If you have any comment, do not hesitate to contact the author at the above adress.

 		 http://dragon.klte.hu/~gundat/rajzprogramok/dprog.html  

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