My software notes

August 26, 2012

[PyMOL] grid mode

Filed under: pymol/ molmol — kpwu @ 2:43 pm
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It is often that we compare different proteins and want to show all aligned proteins in one time.

One popular way shown in scientific papers is to superimpose all structures, however it shows an overlapped “tangle”.  Sometimes such way doesn’t provide a good view for reader.

I am going to show you the “grid_mode” provided in PyMOL. It’s quite useful for PyMOL users to generate high quality “well-aligned” proteins in grid mode.

First,  I load all proteins I want to compare. 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).

Then I use “alignto” command to align all structures to “1PJW” and remove all other un-used chains.

Then, I turn on the grid mode by typing in “set grid_mode, 1“. The PyMOL viewer instantly aligns the 4 proteins in 2×2 grid.

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.

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”.

I frequently see some 2×2 “detailed views” of proteins in papers. I always thought that the author must generate individual figures and then assemble those figures by photoshop or other image editors. I found that PyMOL grid_mode can generate such 2×2 detail view quickly. I like this function A LOT! Here is the example. What I made is to zoom in the 4 proteins and rotate them to proper view for comparison. The output image is ready for publication! (easy, isnt it?)

August 20, 2012

PyMOL on the iPad

Filed under: pymol/ molmol — kpwu @ 9:26 pm
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PyMOL mobile app for iPad released today as posted by PyMOL maintainer at PyMOL mailing list.

Please go to “” to see details.

Or directly go iTunes store to download this App.



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