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Explore Using Pymol to create Porcupine plot for PCA analysis (Modevector.py) with 5,738 views, 16 likes, and 19 comments. Experience the impact of this video content that has captured audience attention.

A simple method to create Porcupine plot for PCA analysis using Modevector.py python scripts Requirement: 1. extreme1.pdb; 2. PML script, 3. modevector.py(python code) Please download the python script from http://www.pymolwiki.org/index.php/Modevectors The PML script goes like this: #----------------START-------------------------------------------------- #change this filename load extreme1.pdb #make sure the python script is in the current directory. run modevectors.py split_states extreme1 modevectors extreme1_0001, extreme1_0050, cutoff=.0, head_length=2, head=0.4, headrgb=(1,.2,.1) ,tailrgb=(1,.2,.1) ,notail=0 set cartoon_trace,1 set cartoon_tube_radius, 0.3 cmd.disable('all') cmd.enable('extreme1_0001',1) cmd.enable('modevectors',1) set ray_shadow,0 #the output is saved as a session file. # after which you can save rayed PNG's. save PCA_porcupine_extreme1.pse,format=pse #-----------END------------------------------------------------- Finally, Load the pml script as follows localuser@XYZ$ pymol PMLscript.pml The vector size , color and shape can be customized. see the Pymolwiki page for details

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