Python script to plot 2D FEL

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 The basic instructions remain same as FEL 3D plots. 

These plots are published in Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1





Fel2d.py

## FEL using plot_surface


import numpy as np

from mpl_toolkits.mplot3d import Axes3D

import matplotlib.pyplot as plt

import random

from matplotlib import cm

from scipy.interpolate import griddata

from scipy.interpolate import Rbf

from numpy import linspace

#from matplotlib.ticker import LinearLocator, FormatStrFormatter

import matplotlib

from scipy import interpolate

import matplotlib.mlab as ml

fig = plt.figure(figsize=None, dpi=300, facecolor=None, edgecolor=None, linewidth=0.0, frameon=None, subplotpars=None, tight_layout=None)

ax = fig.add_subplot(111)

### input file with x,y,z coordinates

x,y,z = np.loadtxt('5wt9gibbs.txt').T 

X,Y = np.unique(x),np.unique(y)

xi = linspace(min(X),max(X),len(X))

yi = linspace(min(Y),max(Y),len(Y))

xi,yi = np.meshgrid(xi,yi)

X1, Y1 = np.meshgrid(X,Y)

print (len(x))

Z = griddata((x,y),z,(X1,Y1),method='cubic')

#surf = ax.plot_surface(X1, Y1, Z, rstride=1,cstride=1,alpha=1,cmap=cm.jet, linewidth=0.0, antialiased=3)

cset = ax.contourf(X1, Y1, Z, zdir='z', offset=-0, cmap=cm.jet, antialiased=3, vmin=0, vmax=18)

### put name of each axis. Cgange fontsize and lablesize accordingly

ax.set_xlabel('PC1',fontsize=12)

#ax.set_xlim(-6, 6)

ax.tick_params(axis="x", labelsize=6)

ax.set_ylabel('PC2',fontsize=12)

#ax.set_ylim(-6, 6)

ax.tick_params(axis="y", labelsize=6)

#ax.set_zlabel('Z axis', fontsize=12)

#ax.tick_params(axis="z", labelsize=6)

#ax.set_zlim(0.0, 12.0)

# Add a color bar which maps values to colors.

#fig.colorbar(surf, shrink=0.8, aspect=20)

#fig.colorbar(surf, shrink=0.5, aspect=20, extend='neither', ticks=[0, 2, 4, 6, 8, 10, 12])

plt.show()



For any queries regarding the script, kindly drop your message in the comments section below.

Please also provide your valuable feedback and stay tuned for more such blogs and scripts!!

Happy Computing!!

Comments

  1. UnknownJanuary 28, 2022 at 12:47 PM

    Thanks.but i how can i have the conformations?

    ReplyDelete
  2. DL COMP-BIO-TECHJanuary 30, 2022 at 5:38 AM

    Hi,

    The low energy conformers can be extracted by:
    1. when u run the pymol script to generate the FEL image.. dont save directly in the folder by the script.. rather let the image open as a window so that u can save it manually..
    2. when image window opens.. mouse over to the basins of your interest, then somewhere on the bottom left side u could see the x and y coordinates of the basin.
    3. search those values in the pca12.dat that contains the time frames also.
    4. Now u wont find the exact values of the coordinate but somewhere near to it. x and y coordinates denotes to mode 1 (PC1) and mode 2 (PC2) values respectively.
    5. likewise u will get the approximate idea of the time frame (mentioned in the first column of the file).
    6. then using any frame extraction method .. u can extract that particular frame from the trajectory.

    ReplyDelete
    Replies
    1. DexterFebruary 15, 2023 at 7:53 PM

      hello, I didn't pca12.dat file. can you pls suggest what steps need to be taken to find out the conformer at that particular ns if the same process has been done through gromacs. Also i tried your code to find the lowest energy bins in spyder ide, but i didn't get the x and y points as you have mentioned, so is there any way to find out the lowest energy regions and save it in a table?

      Delete
  3. Thuy NguyenApril 22, 2022 at 4:04 AM

    Can I ask a question? I have recently done dPCA. Do I need motify the trajectory with -center -pbc -mol -fit rot + trans before analyse dPCA?

    ReplyDelete
  4. AnonymousDecember 22, 2023 at 7:30 AM

    How to save the FEL? I used plt.savefig('pca'). But its showing 0 axis.What should i do?

    ReplyDelete

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