In [2]:

    

%pylab inline


    

    




Populating the interactive namespace from numpy and matplotlib

In [3]:

    

CV_1EX6 = loadtxt('COLVAR_1')
CV_4F4J = loadtxt('COLVAR_2')
HILLS_1EX6 = loadtxt('HILLS')


    

In [37]:

    

Energy = loadtxt('1EX6_energy_3.xvg')


    

In [11]:

    

figure(figsize=[20,50])

amino_acids_1EX6 = ["Glycine-30","Phenylalanine-31","Serine-32",
                    "Valine-33","Serine-34","Serine-35","Threonine-36","Threonine-37"]
amino_acids_4F4J = ["Glycine-30","Phenylalanine-31","Serine-32",
                    "Valine-33","Proline-34","Serine-35","Threonine-36","Threonine-37"]

for i in range(0,8):
    subplot(8,2,(2*i+1))
    plot(CV_1EX6[:,i+2]*180/pi,CV_1EX6[:,20+i]*180/pi,'.')
    xlabel('$\psi$ (degrees)', fontsize=16)
    ylabel('$\phi$ (degress)',fontsize=16)
    title(amino_acids_1EX6[i] + ' Ramachandran Plot', fontsize=20)
    axis([-180,180,-180,180])
    
    subplot(8,2,(2*i+2))
    plot(CV_4F4J[:,(i+2)]*180/pi, CV_4F4J[:,20+i]*180/pi, 'r.')
    xlabel('$\psi$ (degrees)', fontsize=16)
    ylabel('$\phi$ (degrees)',fontsize=16)
    title(amino_acids_4F4J[i] + ' Ramachandran Plot', fontsize=20)
    axis([-180,180,-180,180])


    

In [60]:

    

figure(figsize=[8,6])

distance = CV[:,1]
bias = CV[:,40]
x = range(0,5001)
plot(x,distance)
title('Distance of between two lobes versus the Gaussian count')
xlabel('Number of Gaussians')
ylabel('Distance (angtroms)')


    

    
Out[60]:





<matplotlib.text.Text at 0x10d7efc50>






    

In [36]:

    

figure(figsize=[8,6])

W = .1
s0 = HILLS_1EX6[0,1]
s = HILLS_1EX6[:,1]
sigma = .15
Gaussian = []
for i in range(0,len(s)):
    V = W*exp(-(s0-s[i])**2/(2*sigma**2))
    Gaussian.append(-V)
plot(s,Gaussian, '.')


    

    
Out[36]:





[<matplotlib.lines.Line2D at 0x108caef50>]






    

In [15]:

    

print amino_acids_1EX6[0]
print amino_acids_4F4J[0]


    

    




Glycine-30
Glycine-30

In [41]:

    

plot(Energy[:,0],Energy[:,1])


    

    
Out[41]:





[<matplotlib.lines.Line2D at 0x10a489fd0>]