In [4]:
import MDAnalysis as mda
import matplotlib.pyplot as plt
%matplotlib inline
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from MDAnalysis import *
from MDAnalysis.analysis.align import *
from MDAnalysis.analysis.rms import rmsd
from MDAnalysis.analysis.rms import RMSF
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import MDAnalysis
u = MDAnalysis.Universe('41w_ff.psf','50_frame.dcd')
ref = MDAnalysis.Universe(PSF,DCD) # reference closed AdK (1AKE) (with the default ref_frame=0)
#ref = MDAnalysis.Universe(PSF,CRD) # reference open AdK (4AKE)
import MDAnalysis.analysis.rms
R = MDAnalysis.analysis.rms.RMSD(u, ref,
select="backbone", # superimpose on whole backbone of the whole protein
groupselections=["backbone and (resid 1-29 or resid 60-121 or resid 160-214)", # CORE
"backbone and resid 122-159", # LID
"backbone and resid 30-59"], # NMP
filename="rmsd_all_CORE_LID_NMP.dat")
R.run()
R.save()
import matplotlib.pyplot as plt
rmsd = R.rmsd.T # transpose makes it easier for plotting
time = rmsd[1]
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111)
ax.plot(time, rmsd[2], 'k-', label="all")
ax.plot(time, rmsd[3], 'k--', label="CORE")
ax.plot(time, rmsd[4], 'r--', label="LID")
ax.plot(time, rmsd[5], 'b--', label="NMP")
ax.legend(loc="best")
ax.set_xlabel("time (ps)")
ax.set_ylabel(r"RMSD ($\AA$)")
fig.savefig("rmsd_all_CORE_LID_NMP_ref1AKE.pdf")
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import MDAnalysis
u = MDAnalysis.Universe('41wl_ff.psf','50_frame.dcd')
pdb = "./41wl_ff.pdb"
#ref1 = u.trajectory.
ref = MDAnalysis.Universe('41wl_ff.psf','50_frame.dcd') # reference closed AdK (1AKE) (with the default ref_frame=0)
#mobile = Universe(PSF,DCD)
rmsd(u.atoms.CA.positions, ref.atoms.CA.positions)
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import numpy as np
RMSD = []
backbone = u.select_atoms("protein and (name C or name N or name CA)")
reference = ref.select_atoms("protein and (name C or name N or name CA)")
for ts in u.trajectory:
A = backbone.coordinates()
B = reference.coordinates()
C = rmsd(A,B)
RMSD.append((u.trajectory.frame, C))
RMSD = np.array(RMSD)
print RMSD
import matplotlib.pyplot as plt
ax = plt.subplot(111)
ax.plot(RMSD[:,0], RMSD[:,1], 'r--', lw=2, label=r"$R_G$")
ax.set_xlabel("Frame")
ax.set_ylabel(r"RMSD of Backbone ($\AA$)")
ax.figure.savefig("RMSD.pdf")
plt.draw()
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len(u.trajectory)
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Rgyr = []
protein = u.select_atoms("protein")
for ts in u.trajectory:
Rgyr.append((u.trajectory.frame, protein.radius_of_gyration()))
Rgyr = np.array(Rgyr)
print Rgyr
import matplotlib.pyplot as plt
ax = plt.subplot(111)
ax.plot(Rgyr[:,0], Rgyr[:,1], 'r--', lw=2, label=r"$R_G$")
ax.set_xlabel("Frame")
ax.set_ylabel(r"radius of gyration $R_G$ ($\AA$)")
ax.figure.savefig("Rgyr.pdf")
plt.draw()
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import numpy as np
RMSD_aa = []
current = u.select_atoms("protein and not name H*")
reference = ref.select_atoms("protein and not name H*")
for ts in u.trajectory:
A = current.coordinates()
B = reference.coordinates()
C = rmsd(A,B)
RMSD_aa.append((u.trajectory.frame, C))
RMSD_aa = np.array(RMSD_aa)
print RMSD_aa
import matplotlib.pyplot as plt
ax = plt.subplot(111)
ax.plot(RMSD_aa[:,0], RMSD_aa[:,1], 'r--', lw=2, label=r"$R_G$")
ax.set_xlabel("Frame")
ax.set_ylabel(r"RMSD all atoms ($\AA$)")
ax.figure.savefig("RMSD_all_atoms.pdf")
plt.draw()
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In [28]:
import numpy as np
RMSD_lig = []
ligand = u.select_atoms("(resid 142:146) and not name H*") ## include selection based on user description
#current = u.select_atoms("segname BGLC and not name H*")
reference = ref.select_atoms("(resid 142:146) and not name H*")
for ts in u.trajectory:
A = ligand.coordinates()
B = reference.coordinates()
C = rmsd(A,B)
RMSD_lig.append((u.trajectory.frame, C))
RMSD_lig = np.array(RMSD_lig)
print RMSD_lig
import matplotlib.pyplot as plt
ax = plt.subplot(111)
ax.plot(RMSD_lig[:,0], RMSD_lig[:,1], 'r--', lw=2, label=r"$R_G$")
ax.set_xlabel("Frame")
ax.set_ylabel(r"RMSD of ligand ($\AA$)")
ax.figure.savefig("RMSD_ligand.pdf")
plt.draw()
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mdanalysis.analysis?
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MDAnalysis.analysis.rms.RMSF?
In [106]:
import numpy as np
RMSF_bb = []
backbone = u.select_atoms("protein and (name CA)")
C = MDAnalysis.analysis.rms.RMSF(backbone)
C.run()
C.rmsf[:]
import matplotlib.pyplot as plt
ax = plt.subplot(111)
ax.plot(RMSF_bb[:,0], C.rmsf[:,0], 'r--', lw=2, label=r"$R_G$")
ax.set_xlabel("Frame")
ax.set_ylabel(r"RMSF of Backbone ($\AA$)")
ax.figure.savefig("RMSF.pdf")
plt.draw()
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C.rmsf.shape
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