FAQ of Web3DMol

1. How to show the main structure only?

[ Representation Plane ] -> Het Structure -> Hide

2. How to show a part of the molecule as one representation while another part as another representation?

Fragment is an important concept in Web3DMol.

A fragment is a segment of a chain in a molecule.
A fragment has its own representation mode, color mode, label area and label content.

So, you can add a fragment in [ Fragment Plane ], and customize the fragment in Fragment Dialog.

3. I want a part of the molecule be colored as my favorite color, how to do it?

Using Fragment!
Set the fragment's color mode to User Defined, then set your favorite color.

4. How to remove the water molecules?

[ Tools Plane ] -> Extra Structure -> Remove water molecules

5. What's difference between cartoon variants?

The difference is about the cross section.

Cube's cross section is rectangle.
Strip's cross section is like a playground racetrack.
Ribbon's cross section is oval.
Railway's cross section is like a dumbbell.

6. How to embed Web3DMol into my webpage?

Two ways:
(1) Using HTML's iframe tag;
(2) Including Web3DMol's library, and using JavaScript.

Using iframe tag is a really simple way, the most succinct URL may be https://web3dmol.net/?id=100d&widget=0.
Examples : Using JavaScript, Using iframe

7. Sometimes we use grey rather green to show the Carbon atom, how to change?

[ Configuration Plane ] -> [ Color Category ] -> [ Element ] -> [ C ]

8. I want to save my configuration values rather than setting them again the next time, how to do?

[ Configuration Plane ] -> [ Local Storage ] -> [ Save Config to Local Storage ]
The next time you initialize Web3DMol, the default configuration values will be replaced by your configuration values.

Clicking [ Clear Local Storage ] will clear your configuration values saved at Local Storage.
Clicking [ Recover Default Config ] will recover the default configuration values immediately.

continuously updating ...

Any question about Web3DMol, please contact shimx15@mails.tsinghua.edu.cn.