Customize Gauss View! Part 1 [Expand the molecular palette]

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Gauss View is an extremely great molecular viewer (except its price).

The defaults setting is already good enough, but customizing them will make your work even more efficient!

You may find it difficult to hear customization, but no programming knowledge is required!

We’ll show you how to extend the functionality of Gauss View.

This first article describes how to expand the molecular palette!

日本語版記事:Gauss View をカスタマイズしよう!その1【分子パレットを拡張】

Molecular palette

Many people use the molecular palette to quickly build structures on Gauss View. As shown below, the benzene ring button at the top left of the Gauss View menu or the R button next to it are the molecular pallet.

However, this molecular pallet contains some molecules that you have never used.

In my case, I have never used C60 fullerene.

This article shows you how to add the new molecule on your molecular pallet!

Files location

As we mentioned above, there are two kinds of molecular pallet; rings (cyclic molecules) and rgroups.

These files exists in the Gauss View folder, as shown below.

Go to “gv -> data -> rings” folder, there are two folders and a file in rings folder; bitmaps, fragments, and rings.ftb.

Icon pictures with the .xbm extension are in bitmaps folder, and the molecular structure with the extension .frg are in fragments folder.

The file rings.ftb contains the location of each icon image on the molecular pallet and information about which molecular structure corresponds to which icon.

The molecular palette can be extended by creating and editing these three files appropriately. We’ll show you how to prepare files one by one.

1. Creat the icon with the .xbm extension

As you can see the actual molecular pallet of Gauss View, some icons are letters not molecular structure. (For examples, Decalin and C60)

In both cases, please make icon using ChemDraw, and save it with the .png extension.

Next, go to the website Convertio, and convert png file to xbm file.

If the file size of the .xbm is 65 x 65, it will look good when placed on the molecular palette.

2. Creat the .frg file

Draw the molecular structure on Gauss View, then save it as the .gjf extension. As shown below, you need to convert the file format.

In the .frg extension file, first line is molecule’s name and second line is number of atoms.

Regarding coordinates, put a tab blank at the left of each lines. There is also a tab blank between the element name and the x coordinate.

Then write the number of bond of information lines, after the coordinate section. In the above example, total line number of bonding information is 30.

Next, write the bonding information with a tab blank on left side.

The bond information of .frg is quite similar to that of .mol2 file. We recommend to convert gjf file to mol2 file, then copy the bonding information from mol2 file.

3. Edit the .ftb file

The .ftb file format is
“Molecular name”, Icon file name, Molecular structure file name, Column, and Row. (left to right)

As shown above, the newly created triquinane is specified at last line. Then, it is displayed in the 0th row of the 6th column on the molecular palette.

When you add new molecule on your molecular pallet, increase the number of nItems at 4th line of .ftb.

Summary

You can customize the molecular pallet using ChemDraw, Convertio, GaussView!

For organic chemists, we recommend you to add large ligands and protecting groups to molecular pallet.

For researchers working on natural products, we recommend to add basic molecular skeleton to the molecular pallet.

Note that you can also customize the rgroup’s molecular pallet in the same way. In that case, use “?” for the atom that connects to the main structure.

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