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Guide To Image Clipping and SKC Drawing

1. The document provides guidance on clipping images from patent drawings and creating SKC files for chemical structures. 2. Key steps for image clipping include selecting the drawing area in MS Paint, cropping out white space, and saving the file with the patent number and counter. 3. When creating SKC files, chemical structures should be drawn one per line using templates and tools, labeled, and saved as files named with the patent number and counter. Up to four structures can be drawn per file.

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Triccia Leah
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100 views

Guide To Image Clipping and SKC Drawing

1. The document provides guidance on clipping images from patent drawings and creating SKC files for chemical structures. 2. Key steps for image clipping include selecting the drawing area in MS Paint, cropping out white space, and saving the file with the patent number and counter. 3. When creating SKC files, chemical structures should be drawn one per line using templates and tools, labeled, and saved as files named with the patent number and counter. Up to four structures can be drawn per file.

Uploaded by

Triccia Leah
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Guide to Image Clipping and SKC Drawing

Image Clipping

1. Open the patent/screen where the drawing or image for rescan is displayed. You may also open
the patent in espacenet.com or right on your kpogen.
2. Hit the Print Screen button
3. Open MS Paint
4. Press CTRL-V or paste
5. Click the Select icon and select the area containing the selected drawing. As much as possible,
minimize the white spaces in the drawing. This means when you select the drawing, crop the
edges as thinly as possible, without removing the labels or parts of the drawing.

6. Click the Crop icon

7. As a rule, do not include the Figure reference number at the bottom.


8. If and when the Figure references are located NOT at the bottom, remove it using the Select
icon and then hit the DELETE button on your keyboard.
9. Save the file as [patent number]-001.TIF
10. Upload the file on KPOGEN by clicking on Choose Files button

SKC Drawing

First thing first – Set the proper format

 Go to Options->Settings
 Standard bond length should be 0.70 cm
 Thickness should be 1.4 pt
 Arrow length is 1.4 cm
 Click Apply and Save

User Interface - Parts of Biovia Draw


A. File Menu
B. Toolbar
C. Template
D. Canvas
A

C
B
A

(A) File Menu

Click F1 to drive you thru the online guide

Menu Item Description


Creates a new canvas tab for drawing structures. You can also use Ctrl+N to open a
New Tab
new tab.
New from
Creates a new canvas tab with the journal or application settings that you specify.
Settings
Open Opens a file. You can also use Ctrl+0 to select and open a file.
Opens a file from a URL such as Dropbox. Requires developer configuration and an
Open from Cloud
account with the cloud storage to use the Open from Cloud option.
Insert Opens a file and adds it to the current canvas.
Closes the application and prompts you to save your work. You can also use Ctrl+W to
Close Tab
save your work and close Draw.
BIOVIA Draw supports the following file formats:
sketch (.skc)
Save (Ctrl+S)
molfile (.mol)
SMILES file (.smi).
Save As... Enables saving an existing file with a new name or saving a new file. You can also use
(Ctrl+Shift+S) Ctrl+Shift+S.
Save Selection As Enables saving a portion of a drawing to a file. You can also use Ctrl+L.
Save As Image... The following image formats are supported:
Bitmap (.bmp)
Menu Item Description
Graphics Interchange Format (.gif)
Portable Network Graphics (.png),
Tagged Image File Format (.tif)
Windows Metafile (.wmf)
Enhanced Metafile (.emf).
Uncompressed
Allows you to save the drawing in an uncompressed format as a skc, mol, or smi file.
HELM
Enables saving the drawing in a HELM format or skc format. When this option is
Export selected, you are warned that the drawing might not look the same when reopened.
Sequence... When you select to export the structure using the HELM format the drawing is saved
(Ctrl+T) correctly but might not render that same when reopened.
Pre Draw 4 Style
Uses SUP groups to represent the sequence instead of SCSR template atoms. Use the
Pre Draw 4 style when supporting applications that do not support the advanced
features of the current version of BIOVIA Draw.
The following sequence formats are supported:
FASTA
Import Swiss-Prot
Sequence... HELM
XHELM
EMBL
Launch HELM
Use for import and export of HELM format.
Editor
SDF Utility
Launches utility panel that allows you to convert to and from SD files.
(Ctrl+Shift+D)
Print... (Ctrl+P) Prints the canvas that you see.
Print Preview...
Provides a preview of the canvas when printed.
(Ctrl+Shift+P)
Print dialog where you can select your Printer, Print Range, and Number of Copies.
Printer Setup... You can also select more advanced settings such as Paper size, Paper source,
Orientation and so on under the Properties button.
Displays the Page Setup dialog where you can configure settings for Paper size, Paper
Page Setup...
source, Orientation and Margins.
Exit Closes BIOVIA Draw without transferring the structure.

(B) Toolbar
Tool Name Icon
Atom Toolbar tool and Atom Tool

All-Purpose Drawing (Default)

Arrow
Tool Name Icon
Atom-Atom Mapping

Bracket

Chain

Chemical 2D Rotate Tool

Chemical Flip Tool

Circle

Circular Arc

Create Markush Structure or Query

Create Rgroup Label on Structure


Create Attachment Point on Building
Block
Delete Atom-Atom Mapping

Double Bond

Double Either Bond

Down Bond

Down Wedge

Either Bond

Ellipse

Elliptical Arc

Eraser

Haptic Bond

Lasso

Line

Molecule Select Tool

Multibond
Tool Name Icon
Non-Chemical Bracket

Pan

Plus

Polygon
Properties
Rectangle

Markush Bond

Rotate 3D Structure

Rounded Rectangle

Select
Sequence Template Manager
Sequence Tool

Sequence Tool: DNA

Sequence Tool: RNA

Sequence Tool: Create Crosslink

Sequence Tool: Create Chain

Sequence Tool: Edit Chain


Sequence Tool: Custom Modification
Browser
Single Bond

Spline

Text

Template

Triple Bond

Up Bond
Tool Name Icon
Up Wedge

Zoom

(B) Template
You can save your time by importing pre-drawn structures from the template directort.

Parts of a Drawing
Structure drawing

Structure label

Reference Description
Drawing This is the actual chemical structure drawn; May contain rings, atoms,
bonds, arcs, brackets and arrows
Label This will be the label of the drawing; Make sure that the label you
specify here matches those that you indicate in the abstract

Classification of Chemical Structures

Classification Description
Simple and Easy These chemical structures are easy to draw and would normally consume only
an average of 1-5 minutes to draw, from simple benzene rings to amino acids.
Several examples are shown below.

Moderate These structures would normally be processed in 5-15 minutes. Several


examples are shown below.
Difficult and Hard These are very complex structures and are very time consuming to draw. These
would normally take an average of 15-60 minutes to draw, owing to the size,
complexity, shape, orientation and rotation. Several examples are shown
below.

Creating an SKC file

1) Open the patent containing the structure to draw.


2) Recreate the structure by using the template and toolbar tools.
3) Structures should be drawn in a single line. Additional structures that cross past the margin or
window should be drawn in another SKC file. If a single chemical structure cross past the
window, it is acceptable. There is no need to resize the whole structure so that it would fit inside
the window. In no case should you resize the structure as we need to adhere to standard bond
length (Please refer to First thing first – Set the proper format)
Structures should be drawn in a straight line and should not go past the margin

4) You can only draw up to 4 chemical structures in a single SKC file. If the abstract references
more than 4 chemical structures then it should be drawn in additional SKC files when necessary.

Only 4 structures should be drawn in an SKC file; it should not be drawn past the margins

5) Once you have finished the structure, don’t forget to label the structure. The label should be the
same name that you referenced in the abstract.
6) Enclosed the labels in open and close parenthesis.

7) From the File Menu, click Save As and type the patent number of the file minus the hypen and
include a suffix counter, e.g. JP2017149005A-001.skc from JP2017149005-A. The succeeding
drawings are filenamed JP2017149005A-002.skc, JP2017149005A-003.skc, and so on.

Adding a Structure Reference in the Abstract

8) Insert the filename of the SKC file in the specific abstract fields where the structures were
referenced in the abstract. See example below.
9) All structures indicated in a specific abstract field should be drawn.
10) Structures from the other abstract field(s) should be drawn in a separate SKC file.
11) Make sure that the filenames are written correctly as this will fail during the validation process if
there is a mismatch between the filename of the SKC files and the filename indicated in the
abstracted.

Types of Chemical Structures

Type Description
Close (Whole) These are complete structures where smaller structures attach to. Does
not have attachment points. See example below:

3 31 32
R Z Z NCS

Open (Partial) These are structures with attachment points which need to be attached
to another structure to make it whole. See example below (Z 31 structure
should be drawn with attachment points or asterisks):

Z31 = * *
Practice

Try to practice and draw the following simple structures:

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