Loading models

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Loading models from library

• by structural parameters (acyclic hydrocarbons, organic compounds of oxygen)
• compounds found in essential oils (350 compounds)
• other compounds (cyclic hydrocarbons, water, crystals)

Loading a model by structural parameters

Steps:

1. Menu File, submenu Load from database. A toolbar appears.

2. Select type compound type from the list. Available types:

A list of structural parameters will appear, dependent on the type chosen.

3. Select values of structural parameters. Parameters:

• chain length (Chain length) - for all types, up to 10
• position of double bond (Double bond at) - for alkenes and halogenoalkenes
• position of triple bond (Triple bond at) - for alkines and halogenoalkines
• position of up to two halogenes (Halogene at, Halogene 2 at) - for halogenoalkanes, halogenoalkenes and halogenoalkines
• position of hydroxy group (Hydroxy at) - for alcohols
• position of ketone group (Ketone at) - for ketones
• secondary chain length (Chain 2 length) - for ethers and esters of carboxylic acids

4. Click on Load button. The model will appear.

Loading a model of compounds of essential oils

Steps:

1. Menu File, submenu Load from database. A toolbar appears.

2. From the compound type list select compounds from essential oils. Alphabetical list of 350 compound names appears.

3. Select a compound name from the list of compounds.

4. Click on Load button. The model will appear.

Loading other models

Steps:

1. Menu File, submenu Load from database. A toolbar appears.

2. From the compound type list select OTHER. Alphabetical list of compounds appears.

3. Select a compound from the list of compounds.

4. Click on Load button. The structure will appear.

Loading multiple models

Menu File, submenu Load from database. A toolbar appears.

By default, every loaded model replaces the one(s) previously loaded. You can clear the loaded models by clicking the Clear button.

To add more models to those already displayed, tick the Add to existing checkbox.

When multiple models are displayed, you can manipulate (rotate or move) each one separately using Manipulate models buttons, enabling positioning of multiple models:

• rotate model: click on one of the models and drag for free rotation
• translate model: click on one of the models and drag to move
• turn off manipulation - rotation and translation are turned off; only scene rotation is available (click and drag anywhere)

Steps:

1. Load the first model

2. Tick Add to existing model

3. Load the second, third,... model

4. Arrange models

Loading a model from a file

Steps:

1. Menu File, submenu Load from file. Dialog box for file upload will appear.

2. Select a file from your computer (acceptable chemical formats mol, pdb, xyz, spt,...).

3. Select Load on the dialog.

Saving models

Currently displayed models can be saved as model files (only structure), as state (structure and display parameters) or as image.

Save structure

Menu File, submenu Save model to file. File name dialog box appears. File will be saved in the mol format  (atom coordinates and bonds) to the Downloads folder.

Save structure and display

Menu File, submenu Save state to file. File name dialog box appears. File will be saved to the Downloads folder.

If the file was downloaded from database (as opposed to created from scratch), link to the database will be also saved within the file. If the file was edited, edits will be saved.

Save image

Menu File, submenu Save image to file. File name dialog box appears. File will be saved to the Downloads folder.