Michelanglo — PDB

Convert a PDB code or file (PDB/mmCIF) to an interactive NGL viewport

Step 1 Load structure

For greater control see PyMOL converter. If in need of a demo, you could try the PDB code 1UBQ (ubiquitin) as it has a fun helix to look down at 22-34 or 1GFL (wild type GFP), which has a chromophore at 65-67:A.

PDB code

Weird PDB code

or

Upload file

Choose file

Please upload a valid pdb/mmCIF file.
Step 2 Configure initial view

Choose how the view of the protein should look like when page first loads (initial view) by either using the view-building interface or by editing the tag directly. See documentation for more information.

Residue numbering mismatch
The residue numbers in the PDB file and those in Uniprot differ for some chains
Click this to make the residues in the structure to match Uniprot (irreversible):

Predicted model
This structure is from Swiss-Model. It is a computational model generated by threaded against a crystallised structure (Swissmodel docs ). It may be incorrect. E.g. missing ligands or broken cysteine bonds.

Engineered residues

The protein contains engineered residues () . Click this to make the residues in the structure to match Uniprot (irreversible):
Initial view
Zoom to

domain residue clash surface bfactor auto default orientation

Selection

Color

Title

Radius

Tolerance

Show ligands

Orientation

Freeze

The orientation of the protein differs from the stored one above.

Add additional residue selections
<span class="prolink" data-toggle="viewport">Change a setting!</span>
Other

Mutagenesis

The mutations will be in the main structure after the page is created. If the mutated residue is shown in the initial view, it is suggested to use 'clash' focus mode. To show first the wild type structure on page loading but allow the visitor to toggle to a mutation, create a page with no mutations and then add them in the edit menu.

Chain

List of mutations

Chain removal

The asymmetric state of crystal structures do not always reflect the oligomerisation of the protein or there may be unneeded chains.

Chain

Remove waters and ligands

Crystallographic waters are that kept in an ordered position by the protein. Often chemicals that aid in crystallisation are similarly found. Natural ligands will not be removed (cf. blacklist).

Remove waters

Remove crystallisation compounds
Step 3 Create

Create page. Note that chosen initial view cannot be changed once created.

This tool allows you to create custom anchor elements that control the protein. See documentation for more.

Zoom to

domain residue clash surface bfactor auto default orientation

Selection

Color

Title

Radius

Tolerance

Show ligands

Orientation

Freeze

The orientation of the protein differs from the stored one above.

Add additional residue selections

<span class="prolink" data-toggle="viewport">Change a setting!</span>

Michelanglo — PDB

Convert a PDB code or file (PDB/mmCIF) to an interactive NGL viewport

Step 1 Load structure

Step 2 Configure initial view

Residue numbering mismatch

Predicted model

Engineered residues

Initial view

Other

Mutagenesis

Chain removal

Remove waters and ligands

Step 3 Create