My software notes

August 26, 2012

[PyMOL] grid mode

Filed under: pymol/ molmol — kpwu @ 2:43 pm
Tags: ,

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?)

Advertisements

2 Comments »

  1. […] Tips of “grid mode” can be found in my earlier post: [PyMOL] grid mode. […]

    Pingback by [PyMOL] side-by-side comparison of 3 electrostatic surface potentials « My software notes — September 18, 2012 @ 2:22 am | Reply

  2. My coder is trying to convince me to move to .net from PHP.
    I have always disliked the idea because of the expenses.
    But he’s tryiong none the less. I’ve been using Movable-type on
    a number of websites for about a year and am worried about switching to another platform.
    I have heard great things about blogengine.net.
    Is there a way I can import all my wordpress content into it?
    Any kind of help would be really appreciated!

    Comment by syracuse crossfit gym — April 7, 2014 @ 5:36 am | Reply


RSS feed for comments on this post. TrackBack URI

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Blog at WordPress.com.

%d bloggers like this: