Chemtool(How to draw chemistry):MOST: Difference between revisions

Revision as of 13:52, 25 September 2016

Chemtool is useful for drawing chemistry intended for scientific papers

Introduction

Link to the development page with various versions and descriptions the version 1.6.15 is the most current during the writing of this methods page.

In Literature: Receptor Rigidity and Ligand Mobility in Trypsin–Ligand Complexes

Chemtool is a useful program when there is a need to create models of molecules for scientific papers. While it is possible to draw and label complex molecules, Chemtool also has built in templates to make this process easier. Specifically, for carbocycles, sugars, heterocycles, and amino acids.

Chemtool has the capability of locking in different bond angles, superimposing text, rotating and copying already built molecules, and calculating molecular weight.

Installation

Go Here and click the download link

Once the .zip file has finished downloading move it to an appropriate directory and unpack it

Chemtool doesn't need to be installed to be accessed, simply run the Chemtool.exe file to access the program

Explanation of use

The first 5 buttons(1-5) from the left allow a set change in angle of carbon chain when chosen
The next three buttons(6-8) signify a change in orientation of text when added, justify left, middle, or right.
Button(9) allows a change in text font(bold or normal)
Button(10) allows for different bonding images to be displayed when connecting atoms, primarily single, double or triple bonds will be used.
Button(11) allows for change in coloration of bonding between atoms for color coding
Button(12) allows for the created bond type with buttons (1-5) to be modified selecting a bond from button (10)
Button(13) allows for the marking of molecules or sections of molecules. Molecules must be marked before they can be manipulated with the following 8 buttons (14-21)
Button(14) may be used to translate molecules or their sections
Button(15) may be used to rotate molecules or their sections
Buttons(16 and 17) may be used to flip the marked molecules or their section horizontally or vertically.
Button 18 may be used to copy a marked molecule or their sections
Button 19 may be used to scale molecules to different sizes
Button 20 may be used to create several kinds of brackets around the marked molecule or sections
Button 21 may be used to remove duplicate bonds and in general is used to clean up molecules for publishing
The text bar below the buttons may be accessed to superimpose text upon the chemistry drawn
When satisfied with the drawing, export it as a bitmap, and if that doesn't work then do a screen capture.

Shutdown

After exporting(saving) the created molecule simple close the program

@@ Line 1: / Line 1: @@
 {{MOST}}
-<!-- Comments that appear only in the edit view are formatted like this. -->
-<!-- These comments are offered as an aid as you get started. Remove as you wish. -->
-<!-- next line is the code for inserting an image; delete if you don't have an image yet -->
 [[File:Imageneeded.png|thumb|right|Sample photo caption.]]
+<center>''Chemtool is useful for drawing chemistry intended for scientific papers ''</center>
-<center>''You can put an abstract (a brief description of your method) here and the text you would copy into an article. ''</center>
+==Introduction==
+[http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html Link to the development page with various versions and descriptions] the version 1.6.15 is the most current during the writing of this methods page.
+In Literature: [http://dasher.wustl.edu/bio5476/reading/proteins-58-407-05.pdf Receptor Rigidity and Ligand Mobility in Trypsin–Ligand Complexes]
+Chemtool is a useful program when there is a need to create models of molecules for scientific papers. While it is possible to draw and label complex molecules, Chemtool also has built in templates to make this process easier. Specifically, for carbocycles, sugars, heterocycles, and amino acids.
+Chemtool has the capability of locking in different bond angles, superimposing text, rotating and copying already built molecules, and calculating molecular weight.
-==Introduction==
-[http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html Link to the development page with various versions and descriptions]
 ==Installation==
+# Go [http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html Here] and click the download link
+{{clear}}
+[[File:Imageneeded.png|thumb|right|Sample photo caption.]]
+{{clear}}
+# Once the .zip file has finished downloading move it to an appropriate directory and unpack it
+{{clear}}
+[[File:Imageneeded.png|thumb|right|Sample photo caption.]]
+{{clear}}
+# Chemtool doesn't need to be installed to be accessed, simply run the Chemtool.exe file to access the program
 ==Explanation of use==
-==Example==
-==Shutdown==
+[[File:Imageneeded.png|thumb|Sample photo caption.]]
+# The first 5 buttons(1-5) from the left allow a set change in angle of carbon chain when chosen
+# The next three buttons(6-8) signify a change in orientation of text when added, justify left, middle, or right.
+# Button(9) allows a change in text font(bold or normal)
+# Button(10) allows for different bonding images to be displayed when connecting atoms, primarily single, double or triple bonds will be used.
+# Button(11) allows for change in coloration of bonding between atoms for color coding
+# Button(12) allows for the created bond type with buttons (1-5) to be modified selecting a bond from button (10)
+# Button(13) allows for the marking of molecules or sections of molecules. Molecules must be marked before they can be manipulated with the following 8 buttons (14-21)
+# Button(14) may be used to translate molecules or their sections
+# Button(15) may be used to rotate molecules or their sections
+# Buttons(16 and 17) may be used to flip the marked molecules or their section horizontally or vertically.
+# Button 18 may be used to copy a marked molecule or their sections
+# Button 19 may be used to scale molecules to different sizes
+# Button 20 may be used to create several kinds of brackets around the marked molecule or sections
+# Button 21 may be used to remove duplicate bonds and in general is used to clean up molecules for publishing
+# The text bar below the buttons may be accessed to superimpose text upon the chemistry drawn
+# When satisfied with the drawing, export it as a bitmap, and if that doesn't work then do a screen capture.
-== References ==
+==Shutdown==
-<!-- This code is for placing the citation you included above.  If you did not use the <ref> code, please delete this. -->
+# After exporting(saving) the created molecule simple close the program
-<references/>
 [[Category:MOST methods]]