世界最大邮轮Ur Manual
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Copyright © 2009-2012 Claude Y. Legault Rev.C
CYLview 1.0b
Copyright © 2009-2012 Claude Y. Legault
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to u the Software as obtained. The above copyright notice and this permission notice shall be included in all copies of the Software.
Disclaimer
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Introduction
Thank you for trying CYLview BETA. Plea email any problems or suggestions to claude_legault@cylview.
Installation
Windows urs
Run the installer and lect the installation directory.
Note: For CYLview to function properly, it must be installed with administrative privileges, as the command-line version of POVray forces the creation of the rendered image file in the CYLview directory.
Mac urs
Drag and drop the CYLview.app icon in your Applications folder.
CYLview is currently only compatible with Intel bad Mac computers. Moreover, the current version
of CYLview runs using X11 bad Tkinter. X11 rver must then be installed and running properly on your computer in order to CYLview to run. The X11 rver can be found on your installation CD at the following location:
/System/Installation/Packages/X11Ur.pkg
Following installation, simply start the X11 rver and let it run in the background. Note: X11 rver should be installed by default on Mac OS Leopard (10.5) systems. However 10.5.6+ urs might have to install XQuartz (xquartz.macosforge) OpenBabel
CYLview can u the file conversion capabilities of OpenBabel. If you have OpenBabel installed on your computer, CYLview will automatically u it to open 90 file formats. You can obtain OpenBabel at openbabel/wiki/Install.
Overview of the Interface
CYLview was designed to integrate all its features into a single window, preventing unecessary dispersion of various workspaces and toolbar windows around the screen. The interface is divided into 5 main ctions:联合办厂项目
A Molecular workspace
This is where the 3D reprentation of the molecular structure, including all the customizations (highlights, labels, etc.), will be reprented.
B Menu Bar英语的发展史
Selecting a menu will reveal its various options underneath.
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C Menu Options
All the available options for the lected menu bar will be displayed in this ction.
D E B C
A
D Toolbar
They are the basic functions of CYLview. With them, it is possible to rapidly break or form bonds of different types as well as label bond distances, angles and dihedral angles. After clicking one of tho buttons, the molecular workspace will enter active lection mode– atoms can be lected by clicking on them.
Plea note that the are toggles, they will remain active until you press escape (ESC).
Bond functions: As two atoms are lected, CYLview will perform the action of the button currently lected. Here are the functions:
Break Remove the bond between the lected atoms
Full Create a full bond.
TS Create a either mi-transparent or dashed bond.
DYNTS Create a dynamic TS bond, its appearance is modified as
the atom-atom distance changes. This is uful to make
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molecular dynamics or IRC movies.
Dative Create a mi-transparent grey bond.
Inter Create a black dotted interaction bond.
Thin Create a thin bright green bond.
Newm Create a Newman projection on the lected bond.
Label functions: CYLview will label bond distances, angles and dihedral angles. The label will be created once enough atoms are lected to make the measurement.
? Button: CYLview will return a measurement value, as two to four atoms are lected, which will result automatically in a value of distance, angle or dihedral angle.
Auto Label: This is a toggle that will activate auto-labeling. When enabled, it will automatically add a distance label to any bond that is created.
3D: Toggle this button to generate red-cyan anaglyphs of your structures.
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