How to select substructure in the Online 3Dmol Viewer?

You can use the select={Selection} URL parameter to select a substructure in the loaded molecule and specify a different style than the whole molecule.

https://3dmol.org/viewer.html?select={Selection}&style={Style}&select={Selection}&style={Style}...

Each {Selection} can use the following syntax:

select={key:value;key:value;...}

There are 2 types of "key"s supported in the online viewer:

1. Non-AtomSpec selection keys:

all - Select the entire molecule. This is the default.
invert:{true|false} - If "true", inverts the meaning of the selection.
expand:{number} - Expands the selection to include all atoms within a given distance.
byres:{true|false} - If "true", include any residues containing selected atoms.
...

2. AtomSpec selection keys:

resi:{number} - Residue number for protein molecules. For example: resi:100.
resn:{name} - Residue name for protein molecules. For example: resn:TYR.
chain:{letter} - Chain letter for PDB data files. For example: chain:B.
...

For example, enter the following URL in Web browser.

https://3dmol.org/viewer.html?pdb=1YCR&style=cartoon&select=chain:B&style=stick&select=resn:TYR&labelres=

The loaded PDB file will be displayed with the following selections and their styles:

1. "style=cartoon" - Display the entire molecule in "cartoon" style.

2. "select=chain:B&style=stick" - Display the chain B in "stick" style.

3. "select=resn:TYR&labelres=" - Display the TYR residues with residue labels.

⇒ "select=resi:..." - Select Protein Residues by Numbers

⇐ "style=..." - Specify Display Style in 3Dmol Viewer

⇑ Using Online Server of 3Dmol Viewer

⇑⇑ 3Dmol.js FAQ