PyMOL visualising e2 rotamers


This morning whilst writing some reports I wanted to show some rotamer populations of my spin label attached to the protein. Whilst MMM provides visualisation, and having had discussions with Jeschke I understand just how difficult it is to do, I do not consider them to be of publication standard. For this reason I needed to come up with something.

So first up do all the calculations in MMM as per normal but make sure you save your statistics.

Then load the protein PDB into PyMOL in the usual methods.

Once open load the MMM rotamers file using the File > Open menu; it should be something like rotamers__PDB-ID__CHAIN__MODEL_RESIDUE_LABEL_TEMP.pdb

Rename the rotamer object to something more useful and user friendly

PyMOL> set_name rotamers__PDB_ID__CHAIN__1_AA_LABEL_TEMP,rotamers

Now hide everything

PyMOL> hide *

Show the protein as a cartoon

PyMOL> show cartoon

Select the rotamer library and show it as sticks

PyMOL> show stick, rotamers

Now hide rotamers with an occupancy of near zero; ie less than 3%, but experiment until you get a sensible number on screen normally in the range of 1-5 %

PyMOL> hide stick, q <0.03

Now we make nice ball and stick models by shrinking stick radius, turning on spheres and setting their size to quite small. Remember to change the hide sphere line to match the number in the hide stick section

PyMOL> set stick_radius, 0.1
PyMOL> show spheres, rotamer
PyMOL> hide sphere, q <0.03
PyMOL> set sphere_scale, 0.15
PyMOL> set sphere_quality, 4

Hide the hydrogens

PyMOL> hide (hydro)

Add some transparency to the sticks so that all can be seen

PyMOL> set transparency, 0.2, rotamers

Colour the remaining rotamers according to their occupancy

PyMOL> spectrum q,rainbow,rotamer,0.03,0.10

This command uses: q is occupancy, rainbow is the colour palette (see built in colour bars or user generated ones), rotamer is the object to colour, and then we have minimum and maximum for range; if we leave these out then colouring is automatically set, usually between 0 and 1 which shows very little.

We still want to have the oxygen, nitrogen and sulphur coloured in their normal atom colours, so we now use

PyMOL> util.cnc

Don’t forget to ray your images to get all your shadows and rendering before you export your image.