PyMOL: Preparing a morph to visualize conformational changes

A morph is an interpolation of the structural transition between two given states. In this tutorial, we aim to visualize the conformational change of the Y2 receptor between active (pdb id 7yon) and inactive (7ddz) states. Start from the pml file of the superposition tutorial and include the morph command.

Morphing is only available in the licensed Schrödinger PyMOL versions.

Generating morphs and saving these as movies

The morph command has the following syntax:

morph name, sele1 [, sele2 [, state1 [, state2 [, refinement [, steps [, method [, match ]]]]]]]

name = string: name of object to create
sele1 = string: atom selection of first conformation
sele2 = string: atom selection of second conformation {default: <sele1>}
state1 = int: sele1 state {default: 1}. If state1=0 and sele1 has N states, create N morphings between all consecutive states and back from state N to 1 (so the morph will have N*steps states). If state2=0, create N-1 morphings and stop at last state.
state2 = int: sele2 state {default: 2 if sele1=sele2, else 1}
refinement = int: number of sculpting refinement cycles to clean distorted intermediates {default: 3}
steps = int: number of states for sele2 object {default: 30}
method = string: rigimol or linear {default: rigimol}
match = string: method how to match sele1 and sele2 {default: align}

in: match atoms by "in" selection operator
like: match atoms by "like" selection operator
align: match atoms with align function (with cycles=0)
super: match atoms with super function (with cycles=0)
name of alignment object: use given alignment

Assume we have loaded two conformations as "active" and "inactive" and displayed these as cartoons. To create a morph between from inactive to active, we use the command:

morph morph01, inactive, active

With the default options, the morph consists of 30 states (1 to 30). To create a movie, these states need to be assigned to movie frames with the madd command:

madd 1-30
madd 30-1

This generates a movie of 60 frames in which the inactive conformation is morphed into the active one and back to the inactive conformation. To watch the animation, press the play button (▶) in the movie controls. You can generate the movie via the GUI: Menu: File, Export Movie as. If you play this movie with looping in powerpoint, the movie will show the conformational change over and over again. Determine the correct size with the viewport x,y command. Do not use excessive size, ideally the movie does not have to be rescaled after importing to powerpoint.

If you want the animation to show the inactive and active states for a longer time period, use the following commands:

mset 1 x10
madd 1-30
madd 30 x10
madd 30-1

Tutorial: Generate a movie showing the conformational switch of the Y2 receptor

Generate a morph showing the conformational switch between active and inactive states of the 7yon and 7ddz structures. Start from the superposition that you prepared already.

In my example here I included a transparent surface.

Tutorial: Morph peptide and receptor

In a second example, we want to generate a schematic simplified animation of peptide binding. While the morph switches from the inactive to the active conformation, the peptide YY should bind. To this end, we make a copy of the bound peptide in the active state and shift that 10 Å out of the receptor. We need the following additional commands:

To make a copy of an object use: copy target-object, source-object
copy YYi, YYa

To shift an object (after the view has been set) along the x,y,z directions of the screen (not the pdb coordinate axes):

translate, vector, selection
translate [0,10,0], YYi

In the example linked here I generated two separated morphs for the peptide and for the receptor and they are played synchronously in the movie (if both morph objects are enabled). It might be possible to use both chains in one morph.

Tutorial: Animate the conformational switch for the extracellular and cytosolic halves of the receptor separately after another

In this animation we aim to show the movements of the top part of the receptor first, and next the movement of the cytosolic part. This may have nothing to do with the timecourse of the conformational switch, it is simply a schematic animation to separate the steps of ligand binding and G-protein binding (next morph animation).

To realize this morph movie, we need to generate an intermediate structure, in which the top half of the molecule already has the active state, whereas the bottom half still resides in the inactive state. For this procedure, we will use the update command, which transfers coordinates from one structure to another. The update command will only work if the corresponding atoms have matching segi id, chain id, residue name, residue number, atom name, and alternate conformation id. To this end, we change the chain ids and segids of the inactive state to match those of the active state (we click on the atoms of both objects to understand, what we need to change):

link to pml script file

alter selection, expression
alter (Y2i), segi='E' ; #update will only work if all atoms have identical segi,chain,resn,resi,name,alt!
alter (Y2i), chain='R'

Next, we generate a new object for the intermediate as a copy of the inactive state:

copy target-object-name, source-object-name
copy Y2inter, Y2i ; #generate an intermediate

Next, we determine the approximate boundaries of the two protein halves along the sequence and copy the coordinates of the top half of the active state to the intermediate state:

update target-selection, source-selection
update Y2inter and resi 48-62+99-135+175-230+280-316, Y2a and resi 48-62+99-135+175-230+280-316

Tutorial: Animate the conformational switch for the extracellular and cytosolic halves of the receptor separately after another and show ligand and G-protein binding

In the next example, consecutive binding of the YY peptide and the G proteins shall be animated in parallel to the conformational change of the receptor:

Link to pml script file.

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