Molwin

The program MolWin reads a file with the atomic coordinates and display a molecule. It supports different input formats.

File

Open

Edit

Copy

View

Stereo

ZoomIn

ZoomOut

Center

Options

Plot

Chemistry

Input

Save

Help

About

Tools bar

It is located at the right side of the window.


ViewStereo
Stereo

Show  two stereo projections. To modify a stereo angle select Option | Color | Stereo Angle.


View_ZoomIn
Zoom In

Increase the scale by 10%.


View_ZoomOut
Zoom Out

Decree the scale by 10 %.


ViewCenter
Center

Move the molecule to the center of the screen (approximately).


PlotOptions
Color and plot options

Option	Description

Bond Width	 A width of lines in pixels which used to show bonds.

Bond Color	 A color for bonds.

Rotation Angle	 An angle (in degrees) to rotate the molecule. Increase the angle if you want to speed up the animation.

Sphere Factor	  A radius of the circle which represents an atom with the atomic number n is determined by the product of SphereFactor and Van-der-Waals Radius.

Switches	Description

Show Atoms 	Display circles representing atoms.

Show Hydrogens 	Display hydrogen atoms.

Show Bonds 	Display bonds as sticks.

Label Atoms	Put atomic symbols or atom names (if input format allows them) near corresponding atoms.


ChremistryOptions
Chemistry Options

Option	Description

BondFudge	 see next option. The default value for BondFudge is 1.12 (see acknowledgment).

Atomic Number or Chemical Symbol	Select a chemical element for the following two fields.

Atomic Radius	For some input formats (XYZ) there is no connectivity information in the input file. Two atoms are considered to be connected if

D12 < (R1+R2)*BondFudge ,

here Ri is an atomic radius of atom i and D12 is a distance between atoms.

Van-der-Waals Radius	 The radius of the circle which represents the atom is determined by

SphereFactor* Van-der-Waals radius.

Initially boxes Atomic  Radius and Van-der-Waals Radius are dimmed. Enter a correct atomic radius or chemical symbol and click Radius button. Now you could change both radius.


Input Options

Select input format. See File|Open.


Save Options

To save current options  in the "molwin.ini"  file. To reset to default options erase this file from your WINDOWS directory.


EditCopy
Edit | Copy

The Copy command places an exact copy of the plot window(s) in the Clipboard.

To paste the copied picture into any other program (PaintBrush, for example), choose Edit Paste.


OpenFile
File | Open

Read the file with the atomic data. It should be in one of the following formats:

  XYZ,   Gaussian Output,   PDB


XYZ Format
XYZ format (subset!)

A short description of the subset of XYZ format used by the program.

Line(s)	Description

1	N, a number of atoms .

2	 a comment (ignored).

3...N+2 	atomic coordinates, one line per atom (see below).

The line with the atomic coordinates has four fields in a free format.

Field(s)	Description

1 	atomic number or chemical symbol of the element. Chemical symbol may be followed by an optional number without any space between the symbol and the number. (i.e "C1" but not "C 1").

2--4 	x,y,z Cartesian coordinates.


GaussianOutput Format
GaussianOutput

The output file of the program GAUSSIAN 92 for Windows.


PDB format

 The Brookhaven Protein Databank format.


Help About
Help | About MolWin

Show copyright and version information.


Tools Bar

Icon(s)	Description

X,Y,Z	 Rotate a molecule about the selected axis. To start press the left or the right button for  clockwise or counterclokwise rotation respectively. To stop rotation release the button. The speed of the rotation is detemined by a Rotation Angle.