Molecular dynamics movie

A short instruction: how to make a movie out of a molecular dynamics trajectory with pymol. First you have to import the trajectory. The tricky thing is that pymol will not read multiple xyz's. But at Lightnir's I found that multiple sdf's work. So you start out converting your trajectory into sdf format (for example with openbabel). Then you open that in pymol, adjust the representation and save the movie frames. Either by something like:

set ray_trace_frames=1
set cache_frames=0
mclear
mpng mov/mov

or by doing that in the "Movie" menu.

Now you need a program that makes a movie out of the frames, for example videomach. And that's it.

Here's an example: the ground state zero point vibrations of ethene. Actually a classical simulation of this quantum phenomenon is neither physical nor exciting. But I don't have anything else to show right now.

Glucocorticoid receptor (3)

Again the same molecule with a few more pictures. They were made with the "apple cutting" plugin from Lightnir. It cuts a plane through the protein. The orientation of this plane is not entered manually but chosen automatically by the viewing perspective which is a pretty cool idea in my opinion.

With pymol and this plugin you can quickly visualise a binding pocket and make pictures like this one ...

... or this one ...


... or this one.

Glucocorticoid receptor (2)

I played some more with the receptor from last week. Here are some more images. The trick is setting multi-layer transparency in pymol (Settings - Transparency - Multi-Layer). Rendering takes quite long then, but it looks nice.

You can take a better lock at the ligand inside the binding pocket.


Or you can make this picture which looks kind of cool, I think.


This one shows the opening in the outside surface.


Two commands to mention are:

Changing the transparency of an object ("cha"):
set transparency, .1, cha
I can never quite remember the syntax for that.

Pymol has a nice way of parallelizing the rendering. The downside is that this will stop the whole system. If you want to keep working while rendering in a multicore machine, you can change the maximum threads:
set max_threads, 1


Glucocorticoid receptor

Time for some more pictures. This (1P93 from the pdb) is the glucocorticoid receptor which would for example bind to cortisol. In this case it's a flourinated derivative of it. I did not read the story behind it but my point here is just to show a ligand in its binding pocket.

The whole protein looks like this, the ligand is shown in red.

If you draw the protein with its van der Waals surface, you notice that there is a small opening which is probably the place where the ligand entered the binding pocket.


Apparently the receptor closed again and the molecule is trapped in there.


If you eat away some of the outer amino acids, you can take a better look at the binding pocket.


Or at a semi transparent binding pocket:

Remove some more amino acids that are in the way and it'll look like this.


How do you create those picutres in pymol?

First you select one chain (the fact that there are four chains is just because that's how it crystallizes):
select cha, chain a
If you go for "preset pretty", you can see the ligand and select it. Call it lig. Then you can modify it, give it double bonds, show it as ball and stick model, ...

For the main protein you may want to select the different secondary structures:
select helix, ss h and cha2
select sheet, ss s and cha2
select loop, cha2 and not (ss h or ss s)
Then you can color those the way you want.
If you want a surface, it makes sense to duplicate that chain a and show the duplicate as a surface.
If you want to select the binding pocket, go for:
select pocket, (lig around 5)
Then you can erase some of the amino acids that are in the way.

Of course after doing all this, you have to play around with colors, perspectives and rendering methods.