Dialogs of MarvinSketch

Preferences
Edit Source
Format
Periodic System
Template Library Manager
Create Group
Attach data
Document Settings

Preferences

The Preferences dialog window is located at the Edit menu. It allows you to change many of the MarvinSketch display settings, including look & feel, error highlighting, and object visibility.
All settings are saved and used when the application is restarted.

Display

Atom & Bond labels are used as the default font type and size to labels such as C/T label of bonds, atom query property labels of atoms, etc.
Double bond spacing is a gap between two lines/sticks representing a double or triple bond measured in Angstroms.
Wireframe bond thickness is the width of bonds in wireframe mode. It is measured in Angstroms.
Stick diameter is the width of bonds in stick mode in Angstroms.
Ball radius is the size of atom spheres in Ball draw type, measured in Angstroms.
Look & Feel allows changing the visual appearance of GUI components. The available options are: Java Metal, Motif, JGoodies Plastic, JGoodies Plastic XP, and the native Look & Feels (Windows, Aqua) based on the underlying operating system.
Show Bond in Hand when checked bond types are shown under the mouse cursor like template structures.
Show Lone Pair as Line when checked lone pairs on the canvas are shown as lines.
Show Charge in Circle when checked a circle is displayed around the charge.
MarvinView Layout sets the default layout to Automatic, Molecule matrix or Spreadsheet.
Automatic fog effect turns on the display mode of fading the bonds and atoms corresponding to the changes of the z coordinate in 3D.
Fog effect factor: manual setting of the fading strength. No fog: all regions of the structure is displayed with the same line strength and color. Strong effect: the fading is at its maximum (molecule is only slightly visible at the far end).

Bonds

Down Wedge Orientation allows changing the wedge bond display convention. Down wedge points downward in MDL's convention, upward (at the chiral center) in Daylight's.
Any Bond Line Style offers three different modes to display bonds of unknown types: Automatic, Dashed and Solid. This option can be separately set to be used in MarvinSketch and MarvinView.
Terminal Bond Deletion Method offers 2 ways to delete the terminal bond of a molecule: only the bond is deleted or the terminal atom disappears with the bond.
"Coordinate" Bond Line Style allows changing the type of coordinate bonds from the default ones (arrow for single atom and hashed for multicenter) to solid.

Structure

Highlighting Valence Errors highlights atoms having wrong valences with red underline when it is checked.
Automatic Lone Pair Calculation calculates lone pairs automatically. Make sure View > Misc > Lone Pairs is checked to see the result.
Validate S-groups At Creation disables the S-group types in the drop-down list which would not yield a chemically correct structure. Usage in MarvinSketch.
Carbon Labels options determine the condition of displaying C labels on Carbon atoms.

Always Never At straight angles
and implicit H atoms
Ligand Orders
- Always
- Never
- On R-groups with definitions

Checkers

Move up/down the checker items: the fixing process may depend on the sequence of the checkers. Checking order can be set using the Up/Down buttons on selected checkers.
Add checkers to the list: the default list can be modified by adding other checkers.
Remove checkers from the list: the default list can be modified by removing checkers not needed.
Save checking list configuration: save your custom checking list
Open checking list configuration: open your custom checking list

Services

The Services module provides seamless integration of third-party calculations into Marvin Sketch. You can add and configure the desired calculations in the Services tab. The set service(s) can be used from the Tools > Services menu afterwards.

Set the order of services by moving them up and down using the Up/Down buttons.
Add a new service to the list by the add button. The preference window of the new service will pop up. Read more about setting different services.
Remove the selected service from the list by the remove button.
Import Service Configuration from file. Import a previously set configuration XML file.
Export Service Configuration to file. You can export the set services to a configuration XML file.

Save/Load

Default location: the folder from which to load or to save molecules may be set by the user.
- Startup directory: the folder where the command to start the application was given.
- Last location: the last folder used for opening or saving a structure.
- Custom working directory: a user-defined folder. If a molecule is loaded from another folder, then the file's location will be offered for saving.
Default file format determines which type is offered by default when structures are saved to file.
Save/Load settings
- Save/Load GUI settings (.MRV format) allows storing and loading parameters like background color, font type, etc. beside the structures. This option can only be used with the MRV format.
- Save/Load zoom factor (.MRV format) stores and loads the zooming scale of the structures. This option can only be used with the MRV format.
Recent file entries defines the number of files in the Recent files list in the File menu, with values between 1 and 10.
Image import service URL URL of a server on which a chemical structure recognition program runs can be given.

OLEServer

Edit Source

You can alter a molecule by directly editing its source in the Edit Source dialog window.
The dialog window provides standard clipboard operations and it is also possible to send the source text to the console.
You can view and edit the source in any of the supported file formats. You can also convert it to Java String which allows easy integration of the structure to a custom Java application code.
To change the format of the source, simply select one from the View Menu. If there are more than one molecule on the canvas, setting View as multiple molecules in the View Menu causes each molecule to appear in a separate block in the source. This feature works only in those cases where the selected format is able to handle multiple fragments. After editing the source text, you can send the structure back to the MarvinSketch canvas by invoking File > Import As, and pressing Import on the appearing dialog window. This will close the Edit Source dialog window.

Format

Atoms and Bonds

On this panel there are many options to change the drawing properties of atoms and bonds.

For more information about using structure drawing styles, please visit this link.

Graphics Objects

The drawing properties of graphics objects (text boxes, brackets, lines, etc.) can be changed on this panel.

Periodic System

Periodic Table

Chemical elements are available as buttons on the Periodic Table panel of MarvinSketch.
Atom buttons are arranged according to the standard periodic table layout.
When the mouse cursor is over a specific atom button, the information panel displays the name of the atom, the atomic number, mass, electronegativity and the oxidation states.
When one of the atom buttons is pressed, the corresponding atom can be placed on the canvas. The atom symbol appears under the mouse cursor, while the button is highlighted in this case.

The Atom List and NOT List buttons can be used to create special atom lists that can be used in queries. When one of these buttons is pressed, atoms can be added to the list by pressing atom buttons one after the other. The lists are not cleared when the list buttons become unselected. The atoms of the list are also shown under the mouse cursor above the canvas. See Query Guide for more details about atom lists and not lists.

Four different coloring schemas can be chosen:

CPK: colors the atoms according to the Corey-Pauling-Kultun coloring scheme
Standard state: colors according to the standard state of the element (gas, liquid, solid)
Blocks: colors elements according to the highest-energy electron's orbital (s-, p-, d- or f-block)
Metals/Nonmetals: colors according to the metallic character of the elements (alkali, alkaline earth, metalloid, transition metal, other metal, nonmetal)

Advanced

For the meanings of the buttons on the Advanced tab please refer to the Query Guide.
When the mouse cursor is over a button, a short description appears on the information panel.

Generic query atoms

Name Description

A Any (any atom except hydrogen)

AH Any atom, including hydrogen

Q Hetero (any atom except hydrogen and carbon)

QH Hetero atom or hydrogen (any atom except carbon)

M Metal (contains alkali metals, alkaline earth metals, transition metals, actinides, lanthanides, poor(basic) metals, Ge, Sb and Po)

MH Metal or hydrogen

X Halogen (F,Cl,Br or I)

XH Halogen or hydrogen

Name	Description
A	Any (any atom except hydrogen)
AH	Any atom, including hydrogen
Q	Hetero (any atom except hydrogen and carbon)
QH	Hetero atom or hydrogen (any atom except carbon)
M	Metal (contains alkali metals, alkaline earth metals, transition metals, actinides, lanthanides, poor(basic) metals, Ge, Sb and Po)
MH	Metal or hydrogen
X	Halogen (F,Cl,Br or I)
XH	Halogen or hydrogen

Atom query properties

Adding query properties to structures.

Name Description

.H+ Increase number of total hydrogens (total number of hydrogen substituents)

.H- Decrease number of total hydrogens (total number of hydrogen substituents)

.v+ Increase number of valence (total bond order)

.v- Decrease number of valence (total bond order)

.X+ Increase number of connections (number of substituents including hydrogens)

.X- Decrease number of connections (number of substituents including hydrogens)

.R- Increase number ofrings (number of rings the atom is a member of)

.R+ Decrease number of rings (number of rings the atom is a member of)

.r+ Increase smallest ring size (size of the smallest ring the atom is a member of)

.r- Decreasesmallest ring size (size of the smallest ring the atom is a member of)

.rb+ Increase ring bond count (number of ring bonds next to the atom)

.rb- Decrease ring bond count (number of ring bonds next to the atom)

.s+ Increase substitution count (number of non-H substituents)

.s- Decrease substitution count (number of non-H substituents)

.h+ Increase number of implicit hydrogens (number of implicit hydrogen substituents)

.h- Decrease number of implicit hydrogens (number of implicit hydrogen substituents)

.D+ Increase degree (number of explicit connections; default for "n" is one)

.D- Decrease degree (number of explicit connections; default for "n" is one)

.u Mark as unsaturated atom (atom has double, triple or aromatic bond)

.a/A Mark as aromatic/aliphatic (has aromatic bond)

Name	Description
.H+	Increase number of total hydrogens (total number of hydrogen substituents)
.H-	Decrease number of total hydrogens (total number of hydrogen substituents)
.v+	Increase number of valence (total bond order)
.v-	Decrease number of valence (total bond order)
.X+	Increase number of connections (number of substituents including hydrogens)
.X-	Decrease number of connections (number of substituents including hydrogens)
.R-	Increase number ofrings (number of rings the atom is a member of)
.R+	Decrease number of rings (number of rings the atom is a member of)
.r+	Increase smallest ring size (size of the smallest ring the atom is a member of)
.r-	Decreasesmallest ring size (size of the smallest ring the atom is a member of)
.rb+	Increase ring bond count (number of ring bonds next to the atom)
.rb-	Decrease ring bond count (number of ring bonds next to the atom)
.s+	Increase substitution count (number of non-H substituents)
.s-	Decrease substitution count (number of non-H substituents)
.h+	Increase number of implicit hydrogens (number of implicit hydrogen substituents)
.h-	Decrease number of implicit hydrogens (number of implicit hydrogen substituents)
.D+	Increase degree (number of explicit connections; default for "n" is one)
.D-	Decrease degree (number of explicit connections; default for "n" is one)
.u	Mark as unsaturated atom (atom has double, triple or aromatic bond)
.a/A	Mark as aromatic/aliphatic (has aromatic bond)

Periodic Table Groups

Name Description

Group 1 (IA,IA) the alkali metals or hydrogen family/lithium family

Group 2 (IIA,IIA) the alkaline earth metals or beryllium family

Group 3 (IIIA,IIIB) the scandium family

Group 4 (IVA,IVB) the titanium family

Group 5 (VA,VB) the vanadium family

Group 6 (VIA,VIB) the chromium family

Group 7 (VIIA,VIIB) the manganese family

Group 8 (VIII) the iron family

Group 9 (VIII) the cobalt family

Group 10 (VIII) the nickel family

Group 11 (IB,IB) the coinage metals or copper family

Group 12 (IIB,IIB) the zinc family

Group 13 (IIIB,IIIA) the boron family

Group 14 (IVB,IVA) the carbon family

Group 15 (VB,VA) the pnictogens or nitrogen family

Group 16 (VIB,VIA) the chalcogens or oxygen family

Group 17 (VIIB,VIIA) the halogens or fluorine family

Group 18 (Group 0) the noble gases or helium family/neon family

Name	Description
Group 1 (IA,IA)	the alkali metals or hydrogen family/lithium family
Group 2 (IIA,IIA)	the alkaline earth metals or beryllium family
Group 3 (IIIA,IIIB)	the scandium family
Group 4 (IVA,IVB)	the titanium family
Group 5 (VA,VB)	the vanadium family
Group 6 (VIA,VIB)	the chromium family
Group 7 (VIIA,VIIB)	the manganese family
Group 8 (VIII)	the iron family
Group 9 (VIII)	the cobalt family
Group 10 (VIII)	the nickel family
Group 11 (IB,IB)	the coinage metals or copper family
Group 12 (IIB,IIB)	the zinc family
Group 13 (IIIB,IIIA)	the boron family
Group 14 (IVB,IVA)	the carbon family
Group 15 (VB,VA)	the pnictogens or nitrogen family
Group 16 (VIB,VIA)	the chalcogens or oxygen family
Group 17 (VIIB,VIIA)	the halogens or fluorine family
Group 18 (Group 0)	the noble gases or helium family/neon family

Special nodes

Name Description

LP Lone Pair. This button changes the selected atom to an explicit lone electron pair.

Pol Pseudo atom 'Pol'. This button changes the selected atom to a pseudo atom labelled Pol (polymer).

* This button creates a '*' atom, which indicates an unspecified end group in polymers.

homology groups The drop-down list contains the default homology groups. Detailed list.

Name	Description
LP	Lone Pair. This button changes the selected atom to an explicit lone electron pair.
Pol	Pseudo atom 'Pol'. This button changes the selected atom to a pseudo atom labelled Pol (polymer).
*	This button creates a '*' atom, which indicates an unspecified end group in polymers.
homology groups	The drop-down list contains the default homology groups. Detailed list.

R-groups

These atoms can be used to describe unknown or unspecified molecule parts or to draw R-group queries or Markush structures.

Custom Property

Name Description

R-group Converts the atom to an R-group with the given number (only numerical characters are allowed). Maximum index is 32767. This atom can be used to describe an unknown or unspecified molecule part or to draw an R-group query or Markush structure.

Alias The given value is shown as atom label but the atom itself does not change.

Pseudo The given value is shown as atom label and the type of the atom is changed to 'Any'.

SMARTS Converts the given value to a complex SMARTS query molecule or atom. If the cursor is kept over the canvas during typing, the conversion can be seen on-the-fly.

Value Adds the given value to an atom as a custom property ("Atom value").

Name	Description
R-group	Converts the atom to an R-group with the given number (only numerical characters are allowed). Maximum index is 32767. This atom can be used to describe an unknown or unspecified molecule part or to draw an R-group query or Markush structure.
Alias	The given value is shown as atom label but the atom itself does not change.
Pseudo	The given value is shown as atom label and the type of the atom is changed to 'Any'.
SMARTS	Converts the given value to a complex SMARTS query molecule or atom. If the cursor is kept over the canvas during typing, the conversion can be seen on-the-fly.
Value	Adds the given value to an atom as a custom property ("Atom value").

Template Library Manager

The Template Library is a hierarchic display of template sets.

It contains several template sets by default (such as Generic, Rings, Amino Acids, etc), and a special set called My Templates.

The dialog has buttons to customize template handling. With the help of these buttons you can add and remove template sets to/from the template library, can change order of a given template set, or open the "Options" dialog. The cleaning options of the templates can be set using the last three buttons on the toolbar. With these buttons you can specify how the template will be placed onto the canvas (NoClean, 2D, or 3D). These options can be set separately for each template category. Note, that the buttons are synchronized with the "Template Options" dialog settings.

Template Options

Maximum number of molecules: template sets can contain large number of molecules. This option maximizes the number of structures being loaded from a template set when it is selected in the Template Library. For example if the option is set to 100, only 100 structures will be loaded to memory and displayed in the library, even if the underlying molecule file contained 25000 structures.
Coordinates: this option is to specify an operation affecting the coordinates when the templates are placed on the canvas.
For example result of placing L-Alanine to the canvas with different options:

As in the original
structures Always perform
Clean2D Always perform
Clean3D
Size of templates: the size with which each template is displayed in the library, measured in pixels.
Maximum number of buttons: this determines the maximum number of buttons allowed on the Advanced Templates Toolbar

Adding a new template set to the library

It is possible to add new template sets to the library using the Add Template Set button on the tool bar.
Using the Browse button you can select a directory or a file of the file system. Specifying a directory will create a hierarchic template set containing all subdirectories and files.

It is also possible to specify a location with ftp protocol. The underlying subdirectories and files will be displayed as with the local file system.

Please note that protocols other than file and ftp are not supported. However remote file systems can help to overcome this restriction.

Removing a template set from the library

You can remove template sets from the library using the Remove Template Set button on the tool bar.
The template set will only be removed from the library, without modifying files on the file system.

Create Group

This dialog makes it possible to create a number of groups along with setting their properties. Group drawing in MarvinSketch.

The available groups and their detailed description are available by clicking on the links below:

Displaying charges on groups is described here.

Attach data

Attached data is a custom field assigned to atoms or brackets. It has an identifier string (name) and a value. Furthermore, a query operator can describe different restrictions in queries.
The dialog provides interface to set the properties of such a field.

Further details of attached data can be found in the Query guide.

Attaching data in MarvinSketch is described here.

The Attach Data dialog is customizable; configuration options and a small example can be found here.

Edit properties

Properties may be added and viewed in MarvinSketch. Various properties can be added, but the value is displayed only on the canvas. Detailed description

Document Settings

You can set the number of horizontal and vertical pages in the Document Grid part, and you can also define the title, the page size and the margins in the corresponding sections of this dialog window. Henceforward, the given title will specify the "molecule title" property.


As in the original structures	Always perform Clean2D	Always perform Clean3D