#Pymol tutorial 10 and 11 install#
I used Fink (Mac OSX 10.6.8) to successfully install Gromacs 4.1 but Fink reported problems while installing pygame. However, this plugin requires “PyGame”, “Tkinter”, “PIL (python image library)” and most importantly, Gromacs!
In PyMOL Wiki, there is a “ contact map visualizer” plugin providing users to inspect the protein intramolecular contacts. The output image is ready for publication! (easy, isnt it?) What I made is to zoom in the 4 proteins and rotate them to proper view for comparison. I like this function A LOT! Here is the example. I found that PyMOL grid_mode can generate such 2×2 detail view quickly. I always thought that the author must generate individual figures and then assemble those figures by photoshop or other image editors. I frequently see some 2×2 “detailed views” of proteins in papers. In addition to the 2×2 grid, I also find that 4 proteins can be separated in 4×1 (one raw) way when I expand the window width of “Pymol viewer”. Since the 4 proteins are first aligned by “alignto” command and then are separated to grids, I can move and rotate them at one time. The PyMOL viewer instantly aligns the 4 proteins in 2×2 grid. Then, I turn on the grid mode by typing in “ set grid_mode, 1“. Then I use “alignto” command to align all structures to “1PJW” and remove all other un-used chains. At here I use the envelope protein domain III from yellow fever virus (Dengue virus, West Nile virus, Japanese Encephalitis virus and tick-borne Langat virus). It’s quite useful for PyMOL users to generate high quality “well-aligned” proteins in grid mode.įirst, I load all proteins I want to compare.
I am going to show you the “grid_mode” provided in PyMOL. Sometimes such way doesn’t provide a good view for reader. One popular way shown in scientific papers is to superimpose all structures, however it shows an overlapped “tangle”. It is often that we compare different proteins and want to show all aligned proteins in one time. In order to make right color gradient schemes (in cartoon mode) either using pymol-provided “spectrum” or the “spectrumany.py” script, it better to define the residue ranges (resi xxx-yyy) not use “all”. When water molecules are presented in “sphere” mode, you can see the water molecules are colored from yellow to white. The reasons are 1) water are numbered after 400 (421-800) and 2). I found that using “ spectrumany count, red green blue yellow white, all” will result in the image below.Īll water molecules are colored in white not not shown in the image. Note: In a lot of crystal protein structure PDB files, there are a lot of water molecules as well as some heavy metal ions. In this pymol script, colors are separated by “space”. The example shown at here using command: “ spectrumany count, red green blue yellow white, resi 1-395“. (more pymol built-in color schemes are listed at my older post: example– coloring surface by b-factor).Īfter downloding “ spectrumany.py” and run “spectrumany.py”, one can customize gradient colors on his/her target. The figure below was drew using command “ spectrum count, red_white_blue, all“. Here is the example I created using “spectrumany” to show customized spectral colors of the example protein TBEV envelope protein “PDBV entry: 1SVB”.īy using the built-in command “spectrum”, one can color the envelope protein in 2 or 3 gradient colors or use the “rainbow” to colorful gradient. Saw a post at recent Pymol mailing list and found the nice example of “ spectrumany” at PymolWiki. Steps to “ Draw the electrostatic surface” can be checked at my earlier post, too. Tips of “grid mode” can be found in my earlier post: grid mode. No worry of sizes of molecules if generated separately. I really like the grid mode in PyMOL! No need to use any image editor to assemble 3 potential views. The electrostatic surface views at 3 pH states can be shown easily! Last, assign the potentials to duplicated objects. After that, turn on the grid mode and then duplicate pdb object twice. Draw first protein with one of the potentials. I used APBS web server combined with PROPKA to get calculated pH-dependent potentials (.dx files). PyMOL script is attached after the figure.įirst, the potential maps at three pH states have to be generated. Here is an example using “grid mode” provided in PyMOL to show the charged states of a protein (PDB entry: 1Z66) at pH 4 (left), 7 (center) and 11 (right).
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