scrren_cap8

Advanced Pymol Movie

Here I will give a shortish guide to how I made this ribosome movie  with Pymol.

I knew I wanted to make a movie somehow displaying the expansion segments of the eukaryotic 80S ribosome versus the prokaryotic 70S ribosome. I knew that the majority, if not all, of the expansion segments was added like an additional layer onto a conserved core consisting of the 70S ribosome.

So It seemed obvious to start the movie displaying only the core 70S ribosome and then introduce the the expansion segments as a layer forming around the core thereby yielding the 80S ribosome.

I used the special PDB file of the 80S ribosome I mentioned in a recent post. First of all I had to identify all of the expansion segments, both the protein and the rRNA ones. Luckily for me the groundwork had already been done by others, as the information was listed in the supplementary information  of the original paper on the yeast 80S ribosome structure. By selecting using the segid’s I could quickly generate two PDB files, one containing the conserved core and one containing all of the expansion segments.

The expansion segments constituted a whooping 81 objects in total, so I had to find an easy way of moving them away from the core, so I could let them fly in during the actual movie. Normally I would just use the translate and rotate commands in pymol to move a object to some random position. However I had no desire to do that 81 times, as I wanted each object to come from an unique direction without passing through the core object on its way back. I found that the fastest and most convenient way to do this,  was simply to move each segment manually using the mouse. To do this I had to go into 3-button-edit mouse mode. When in 3-button edit mode, if you press down the shift key on the keyb you can translate an object by using the middle mouse button and rotate  it by using the left mouse button.  When I had moved all the expansion segments away from the core i saved the new positions of the expansion segments into a new pdb file.

To do the scene where the expansion segments fly in I had to align each individual segment to their original  positions on the 80S ribosome. First however I wanted to have all of the expansion segments as individual objects. The fastest way I could find was using a Psico command called split_molecule. Psico is a python module which needs to be installed or imported before its functions becomes usable.  The command “split_molecules” creates a single object for each molecule (defined as covalently connected entities) in the selection. When used on the PDB file  containing the expansion segments I got 81 objects which now only needed be aligned.

After playing around with some of the different alignment options in PyMol I settled for using the CeAlign. CeAlign is a structure based alignment vs the align command which first performs a sequence dependent alignment followed by a structural  alignment. Basically it worked better for me. However CeAlign has a drawback in that it can not align objects containing fewer than 16 residues. But that affected only 4 or 5 of the objects in the expansion PDB file, so I just ignored it.

Now that all the pdb files and alignments were ready I only needed to make the actual movie.

To be continued (maybe)

 


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