Decades later, we owe Warren DeLano and his commitment to open source a great debt. Warren wrote PyMOL, an amazingly powerful and popular molecular visualization tool, but it has many hidden talents.
Perhaps its greatest strength is the use of the open source language, Python, as its control language.
Continue readingWe all love pretty, colourful pictures of proteins. There is quite a variety of programs to produce publication-quality images of proteins, some of the most popular being VMD, PyMOL and Chimera. Each has advantages and disadvantages — for example, VMD is particularly good to deal with molecular dynamics simulations (perhaps that’s why it is called “Visual Molecular Dynamics”?), and Chimera is able to produce breathtaking graphics with very little user input. In my work, however, I tend to peruse PyMOL: a Python interface is incredibly helpful to produce quick analyses.
Continue readingPutting movies into your presentations is the perfect way to cover up a terrible underlying presentation help the audience visualise the systems you are discussing. Static protein movies can enhance an introduction or help users understand important interactions between proteins and ligands. PyMOL plugins, such as emovie.py, help you move beyond the ‘rock’ and ‘roll’ scenes in PyMOL’s movie tab. But there ends the scope for your static structures.
If you want to take your PyMOL movie making skills to the next level, you should start adding some dynamics data. This allows your audience to visualise how your protein dynamics evolve over time and a much easier way to explain your results (because, who likes 10,000 graphs in a presentation!? Even if your R plots look super swish.). For example: understanding binding events, PPIs over time or even loop motion.
The following tutorial shows you how to turn a static PDB structure into a dynamic one, by adding a GROMACS trajectory. Most of the commands you will encounter while making a static structure movie, so should not be too alien.
We can all agree that typing commands into PyMOL can make pretty and publishable pictures. But your love for PyMOL lasts until you realise there is a mistake and need to re-do it. Or have to iterate over several proteins. And it takes many fiddly commands to get yourself back there (relatable rant over). Recently I was introduced to the useful tool of PML scripting, and for those who have not already discovered this gem please do read on.
These scripts can be called when you launch PyMOL (or from File>Run) and iterate through the commands in the script to adapt the image. This means all your commands can be adjusted to make the figure optimal and allow for later editing.
I have constructed and commented an example script (Joe_Example.pml) below to give a basic depiction of a T4 Lysozyme protein. Here I load the structure and set the view (the co-ordinates can be copied from PyMOL easily by clicking the ‘get view’ command). You then essentially call the commands that you would normally use to enhance your image. To try this for yourself, download the T4 Lysozyme structure from the PBD (1LYD) and running the script (command line: pymol Joe_Example.pml) in the same directory to give the image below.
The image generated by the attached PML script of the T4 Lysozyme (PDB: 1LYD)
#########################
### Load your protein ###
#########################
load ./1lyd.pdb, 1lyd
##########################
### Set your viewpoint ###
##########################
set_view (\
-0.682980239, 0.305771887, -0.663358808,\
-0.392205656, 0.612626553, 0.686194837,\
0.616211832, 0.728826880, -0.298486710,\
0.000000000, 0.000000000, -155.216171265,\
4.803394318, 63.977561951, 106.548652649,\
123.988197327, 186.444198608, 20.000000000 )
#################
### Set Style ###
#################
hide everything
set cartoon_fancy_helices = 1
set cartoon_highlight_color = grey70
bg_colour white
set antialias = 1
set ortho = 1
set sphere_mode, 5
############################
### Make your selections ###
############################
select sampleA, 1lyd and resi 1-20
colour blue, 1lyd
colour red, sampleA
show cartoon, 1lyd
###################
### Save a copy ###
###################
ray 1000,1500
png Lysozyme_Example_Output.png
Enjoy!
MOSAICS is suite of sampling methods for molecular simulations of motion of nucleic acid and protein structures. It’s applicability has been demonstrated in simulating large ensembles of nucleic acids (Sim 2012, Minary 2014) and proteins.
Starting with a protein/dna/rna structure you would like to examine, the basic modus operandi of MOSAICS is divided into three parts:
The energy function defines the energy surface with respect to your degrees of freedom (DoFs) and the sampling methodology is supposed to explore the conformational space along DoFs.
One of the main fortes of MOSAICS lies in the ability of defining hierarchichal natural moves. Defining regions of collective motion introduces experimental knowledge and intuition into the simulations, greatly accelerating sampling. Ability to define such regions was one of the main reasons to start the development of the graphical user interface (GUI) for MOSAICS — preliminary version can be seen in the Figure below.
Overview of PymoSAICS in its current form.
Since we are developing the GUI as a plugin for Pymol, we called it PymoSAICS. The initial focus of the project is on nucleic acids due to our interests in the structural effects of epigenetic modifications. As demonstrated in the Figure above, the GUI is divided into three main panels:
Users can upload their favorite structure via PymoSAICS or Pymol and play with the available parameters. The GUI is also an ongoing effort to streamline the available protocols in MOSAICS to shield the user from the many parameters that are available but perhaps not relevant to the simulation at hand.
We are currently starting beta tests of the application which (if you don’t mind not getting any support just yet) is available here, Therefore, if you are interested in becoming a tester please let me know, and you will receive a version around Easter (April-ish)! Contact me via konrad.krawczyk at dtc.ox.ac.uk
This is a little PyMOL script that I’ve used to draw antibody-antigen interfaces. If you’d like a commented version on what each and every line does, contact me! This is a slight modification of what has been done in PyMOL Wiki.
load FILENAME set_name FILENAME, complex set bg_rgb, [1,1,1] color white hide lines show cartoon select antibody, chain a select antigen, chain b select paratopeAtoms, antibody within 4.5 of antigen select epitopeAtoms, antigen within 4.5 of antibody select paratopeRes, byres paratopeAtoms select epitopeRes, byres epitopeAtoms distance interactions, paratopeAtoms, epitopeAtoms, 4.5, 0 color red, interactions hide labels, interactions show sticks, paratopeRes show sticks, epitopeRes set cartoon_side_chain_helper, on set sphere_quality, 2 set sphere_scale, 0.3 show spheres, paratopeAtoms show spheres, epitopeAtoms color tv_blue, paratopeAtoms color tv_yellow, epitopeAtoms set ray_trace_mode, 3 unset depth_cue set specular, 0.5
Once you orient it to where you’d like it and ray it, you should get something like this.
Another largely plagiarized post for my “personal notes” (thanks Justin Lorieau!) and following on from the post about pretty-fication of macromolecules. For my slowly-progressing confirmation report I needed some beautiful small molecule representation. Here is some PyMOL code:
show sticks set ray_opaque_background, off set stick_radius, 0.1 show spheres set sphere_scale, 0.15, all set sphere_scale, 0.12, elem H color gray40, elem C set sphere_quality, 30 set stick_quality, 30 set sphere_transparency, 0.0 set stick_transparency, 0.0 set ray_shadow, off set orthoscopic, 1 set antialias, 2 ray 1024,768
And the result:
Beautiful, no?
Just came across a wonderful PyMOL gallery while creating some images for my (long overdue) confirmation report. A fantastic resource to draw sexy proteins – especially useful for posters, talks and papers (unless you are paying extra for coloured figures!).
It would be great if we had our own OPIG “pymol gallery”.
An example of one of my proteins (1tgm) with aspirin bound to it:
