CYLview - manual

User Manual

Copyright ? 2009-2012 Claude Y. Legault

Rev.C

CYLview User Manual Page 2

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 \to use 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 \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. Please email any problems or suggestions to claude_legault@cylview.org.

Installation

Windows users

Run the installer and select 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 users

Drag and drop the CYLview.app icon in your Applications folder.

CYLview is currently only compatible with Intel based Mac computers. Moreover, the current version of CYLview runs using X11 based Tkinter. X11 server must then be installed and running properly on your computer in order to CYLview to run. The X11 server can be found on your installation CD at the following location:

/System/Installation/Packages/X11User.pkg

Following installation, simply start the X11 server and let it run in the background.

Note: X11 server should be installed by default on Mac OS Leopard (10.5) systems. However 10.5.6+ users might have to install XQuartz (http://xquartz.macosforge.org)

OpenBabel

CYLview can use the file conversion capabilities of OpenBabel. If you have OpenBabel installed on your computer, CYLview will automatically use it to open 90 file formats. You can obtain OpenBabel at http://openbabel.org/wiki/Install.

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Overview of the Interface

A B

C

D E

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 sections:

A Molecular workspace

This is where the 3D representation of the molecular structure, including all the customizations (highlights, labels, etc.), will be represented.

B Menu Bar

Selecting a menu will reveal its various options underneath.

C Menu Options

All the available options for the selected menu bar will be displayed in this section.

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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 those buttons, the molecular workspace will enter active selection mode – atoms can be selected by clicking on them.

Please note that these are toggles, they will remain active until you press escape (ESC).

Bond functions: As two atoms are selected, CYLview will perform the action of the button currently selected. Here are the functions:

Break Remove the bond between the selected atoms Full Create a full bond. TS Create a either semi-transparent or dashed bond. DYNTS Create a dynamic TS bond, its appearance is modified as

the atom-atom distance changes. This is useful to make molecular dynamics or IRC movies.

Dative Create a semi-transparent grey bond. Inter Create a black dotted interaction bond. Thin Create a thin bright green bond. Newm Create a Newman projection on the selected bond.

Label functions: CYLview will label bond distances, angles and dihedral angles. The label will be created once enough atoms are selected to make the measurement.

? Button: CYLview will return a measurement value, as two to four atoms are selected, 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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Bonds Menu

In contrast to the Atoms Menu, the molecular workspace will not be in active mode in this menu. Currently, selection of the bonds can only be done in the Bonds List. Pressing escape (ESC) will remove any current selection.

Bonds List: Contain the list of all the bonds as well as their properties. Bonds can only be selected directly through this list.

Show distances: When checked, the bond lengths will be shown on each bond. Note: These labels will not show when rendering.

Select: Automatically select all bonds of the selected type.

Action on bond(s): Perform the selected action or transformation on all currently selected bonds. Break: Remove bonds. Label: Add distance labels. Full: Full/normal bonds. TS: Transition bonds.

Dative: Dative/complex bonds. Thin: Thin green bonds.

Interaction: Black dotted bonds. Newman: Newman projection.

Change Color: Define a custom color for the currently selected bonds.

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Labels Bond

As for the Bonds menu, the labels can only be selected through the Labels List. Pressing escape (ESC) will remove any current selection.

Labels List: Contain the list of all the current labels. The list indicates to which atom(s) the labels are bounded, their values, and their status (e.g. hidden). You can move the selected label(s) using the keyboard arrows. Using CTRL+arrow will move the selected label(s) using a bigger step increment. Set label(s): Perform the selected action on the currently selected labels.

General Action: Perform the selection action on all labels, regardless of the current selection.

Single Atom Label: When any of these toggle functions are selected, a label will be added to any atom that is selected subsequently. Pressing (ESC) will deactivate any selected function. El : Element

Abs# : Absolute atom number

Rel# : Relative atom number (the value will start from 1 and increase as you select other atoms)

El(Abs#) : Element + absolute atom number in subscript

El(Rel#) : Element + relative atom number in subscript

Custom : The text entered in the Custom entry below will be added as a label to the selected atom.

The custom entry currently accept basic formatting by using (__) and (**) encoding. Example:

O__7 : O7

O**C=O : OC=O

This encoding is still very primitive, you cannot return to normal text following subscript/superscript code.

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Styles Menu

Preset styles: Automatically set up the different visual properties to reproduce the selected style. The Custom styles can be defined in the Custom menu.

Finish: Set the surface finish.

Shiny Plastic Atom Size:

Metal

Normal Small Bond Size:

None

Thick Normal Bond Style:

Thin

Colored Black Silver

Misc (Shadow): If checked, the molecule will cast shadows.

Misc (Quadrants): If checked, quadrants will be drawn on the atoms (for Houkmol style). The thickness of the quadrants can be adjusted underneath the checkbox.

Light orientation: Position of the light with respect to the camera facing the molecule.

Quadrants Color: Define a custom quadrant color. Background Color: Define a custom background color.

Set Focal Point (Focus): Select an atom to define the zone in focus of the rendering. Focus Style: Set the depth of field. Strong means a more shallow depth of field resulting in stronger out of focus areas.

Focus follow selected atom: If checked, the position of the focal point will change according to the position of the atom selected using Set Focal Point. If unchecked, the position is fixed to the coordinates of the atom when it was selected .

Set Fog Depth: Select an atom to define the starting depth of fog in the rendering. Fog Style: Set the density of the fog.

Fog follow selected atom: Same behavior as defined for “Focus follow selected atom”.

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Poses Menu

This menu lets you save differents orientations of your structure so that you rapidly go back to desired orientations and configurations.

Poses List: Saved poses will show in this list, with their defined names. Any pose can be reloaded by double clicking on them.

Name: When a pose is saved, it will be listed under the name set in this field.

Pose: Actions to be applied on poses.

Add: Save the current orientation/settings under the name specified.

Delete: Delete the pose currently selected in the list. Update: Update the pose currently selected with the orientation and settings of the molecule in the workspace.

Copy: Transfer specific properties of the pose currently selected in the list to the molecule in the workspace.

Rotation: Copy the rotation information to the workspace.

Scale: Copy the scale factor to the workspace.

All: Copy both properties to the workspace.

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Anim Menu

This feature lets you rapidly create animation from your structure.

*** You must select one of the screen sizes before rendering the animation, as it must be a perfect 4:3 ratio. ***

Add/Delete/Update: You can build animations containing multiples steps. To add a step simply select a start pose as well as the settings desired and click Add. To delete a step, select it in the list and click Delete. To modify the properties of a step, double-click on it, change the settings, and click on Update.

Name: The name that will be given to the animation step in the list

Parameters common to all animation Start Pose: Select the pose that will serve to build the animation step. It must have been created in the “Poses” Menu.

Duration: Determine the time taken for the animation.

Pause: At the end of the animation step, it will add this delay before the next step.

Transition: Determine if the movement speed is constant, sinusoidal, or squared sinusoidal. It is only applicable to rotation and custom animations. Show labels during transition: By default, the labels are hidden during the animation. This will disable this feature.

Animation type: Selecting one of the three animation options will show extended options for the particular type:

Rotate: This will do a 360° rotation in the chosen sense around the selected axis.

Rock: This will rock the molecule within the given angle span, around the selected axis.

Custom: This option let you generate transitions between selected poses (saved initially in the Poses Menu).

End Pose: Select the pose that will serve as the final orientation. CYLview will interpolate the transition path between start and and end poses.

Path: Determine if the shortest or longest route is used between the two orientations.

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vdW Menu

This menu enables rapid analysis of the Steric contacts present in a structure.

Contact Types: This list is generated automatically as a structure is opened. It represents all the atom pairs in which steric contacts exist. By selecting any of these atom pairs, the contacts will show on your structure. Multiple atom pairs can be selected at the same time. To facilitate the analysis, the contacts are colored by an average of the two atom colors of the contact.

Show dihedral contacts: CYLview does not show vicinal steric contacts. By default, it does not show contacts between atoms of dihedral relationship. When checked, it will show these contacts.

van der Waals threshold: This is the threshold at which CYLview will show the contacts on screen. At 100%, the threshold is summation of the van der Waals radius of the respective atom pairs. As the threshold is lowered, only stronger contacts will show. In contrast, by using a threshold over 100%, it is possible to see probable electrostatic contacts. Individual contacts: This list represents the contacts currently displayed on the molecule. It will show the atoms forming the contact as well as the strength of it. It is currently not possible to select specific contacts in this list.

Show distances: When checked, the contact lengths will be shown on each contact on the molecular workspace.

Note: The contacts bonds and their distance labels will not show when rendering.

Make current contacts permanent: This function will create bonds for all the contacts found in the Individual contacts list, so that they will be rendered.

Bond type to use: The bond type used to create the contacts.

Bond color: Auto will use black, green and grey for the interaction, thin and dative bonds, respectively. Black will force any bond type to be black and average will create the selected bond type in a color that is an average of the elements color of the atom pair.

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Opt Menu

With Gaussian03 and Gaussian09 output files, as you open this menu, it will check if a geometry optimization exists and display it. The slider will represent the number of optimization steps. Graph underneath will represent the Forces or Displacement.

Export XYZ of current structure: The structure currently displayed (highlighted in yellow in the graph) will be saved in XYZ format. The suffix _STEP## will be added to the current file name. If the file already exists, it will not be overwritten.

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Freq Menu

With Gaussian03 and Gaussian09 output files, as you open this menu, it will check if a frequency exists in the file and display the frequencies list. Double-clicking on a specific frequency mode will animate the mode on screen. Animation can be stopped by pressing escape (ESC).

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Scan Menu

This module is used to open either multi-xyz files of molecular dynamics of IRC trajectories, or Gaussian03 and Gaussian09 relaxed scan files. With Gaussian output files, only converged optimization structures will be extracted and the graph will represent these points with relative energy in kcal/mol. The slider will represent the number of converged structures.

In the case of multi-xyz files, every structure must contain the exact same number of atoms. The title section of every xyz structure in a multi-xyz file is defined as:

## (Number of atoms) Title

In the title line, if an energy (in hartrees) is supplied as a second value, separated by at least a space, such as (Value1 Energy), then this energy will be used to display a relative energy value in kcal/mol.

Make Movie: A frame will be rendered for every structure displayed in the graph and a mpeg movie (30 fps) will be created.

Reverse play: The movie will be created from the last frame to the first.

Export XYZ of current structure: The structure currently displayed (highlighted in yellow in the graph) will be saved in XYZ format. The suffix _STEP## will be added to the current file name. If the file already exists, it will not be overwritten.

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