10.2 Viewing Poses in PyMOL

10.2 Viewing Poses in PyMOL

You can open up and view your Alldata file in PyMOL too, if you have created a reordered version of your results file you should use this file instead.

Here we have opened up the AlldataReordered file we made earlier:

In order to perform proper analysis on your results you will need to open the pdb file of the protein that you docked these compounds into, this could be your “protein only.pdb” file or alternatively if you have already made a colour coded pdb file ready for your docking results analysis then you can use this (just make sure it is the same protein crystal structure and that it is optimised).

Below is our AlldataReordered file opened with our pre-made colour coded protein surface pdb file.

A couple things to notice here, firstly the protein is not showing entirely, this is because clipping is on. To turn off clipping and show your whole proteins structure click display, clip, nothing.

The next thing to notice is that the hydrogens are not displaying on your ligands (poses), to add these click on the action menu, click hydrogens, then add (on your AlldataReordered entry in the side menu).

Now you are ready to look through your poses, in the bottom right-hand corner (highlighted below) you can see information on what pose you are viewing (State 10/ 54), here we are viewing pose 10 out of the total 54 poses. You can easily switch between poses by using the arrow keys on your laptop, or you can use your cursor and the arrow buttons below.

Just as with any other entry/selection you can change the colour of your displayed poses (but you cannot individually colour each pose).

In a surface plot file like the one above you can examine the position of each pose within your active site.

Below is the same AlldataReordered file opened in another pre-made colour coded pdb file, displaying all the active site residues.

In this kind of file, you can analyse your poses and measure the distances between points of interest on your ligand and certain residues using the wizard tool (see section 4.4).

Pay attention to when each compound ends, in our file pose 36 is the last compound 1 pose, and so when you get to pose 37 you can make a note that you are now analysing the next compound’s poses (this may sound obvious but in bigger files with hundreds or even thousands of poses you will need to keep track).

Once you have your Alldata file opened with the pdb file you want (e.g. a colour coded one) you can save the PyMOL session as a session file (.pse), then you can come back to it and reopen the session at exactly where you left off whenever you wish.