Guide for PyMOL

Initial steps with PDB

Download PBD ID: 1BTL

rename it as 1btl_raw.pdb

Start PyMOL and load 1btl_raw.pdb

From Display show the Sequence

Sequence is now shown

Click A button next to all and select remove waters

Scroll to the right on Sequence and click on S04

click the A button next to (sele) and click remove atoms

Now we are going to save the new file

Go to File and select Export Molecule

Click Save

Type name as 1btl (without pdb extension) and then select PDB from the menu below and click Save

Now we created 1btl.pdb

(Compare with 1btl.pdb in the Beta-lactamase folder on github)

Make a mutation with PyMOL

Download WT_cript.pdb from PDZ folder on github

Start PyMOL and load WT_cript.pdb

From Display show the Sequence

From Wizard go to Mutagenesis and select Protein

As an example we are going to make the S102Y mutation

From the Sequence click on S102. This will select residue S102 and show options on the right panel

On the right panel click No Mutation and from the new panel select TYR

Using the arrows at the bottom of the right panel select a side chain rotamer with least amount of clashes (shown as red regions on the protein). After selecting the rotamer, first click Apply then click Done

Go to File and select Export Molecule

click Save

Type the name of the new pdb file as WT_cript_S102Y (without pdb extension) and then select PDB from the menu below and click Save

Now we created WT_cript_S102Y.pdb