def main():
## trjconv -f 2LZM_wt.trr -o 2LZM_wt_trjconv.pdb -s 2LZM_wt_MD.tpr -skip 10 -sep
fd = open('2lzm.pdb', 'r')
lines1 = fd.readlines()
fd.close()
lines2 = []
for line in lines1:
record = line[:6].strip()
if record in [
'HELIX',
'TURN',
'SHEET',
]:
lines2 += [line]
for i in range(50):
fd = open('%i.pdb' % (i), 'r')
lines = fd.readlines()
fd.close()
lines = lines2 + lines
fd = open('nma%i.pdb' % (i), 'w')
fd.writelines(lines)
fd.close()
stop
import sys, os, numpy
sys.path.append('/home/people/tc/svn/tc_sandbox/quakes/')
import phipsi_comparison
sys.path.append('/home/people/tc/svn/tc_sandbox/misc/')
import phipsi_plot
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
d_residues = {
'ALA': 'A',
'CYS': 'C',
'ASP': 'D',
'GLU': 'E',
'PHE': 'F',
'GLY': 'G',
'HIS': 'H',
'ILE': 'I',
'LYS': 'K',
'LEU': 'L',
'MET': 'M',
'ASN': 'N',
'PRO': 'P',
'GLN': 'Q',
'ARG': 'R',
'SER': 'S',
'THR': 'T',
'VAL': 'V',
'TRP': 'W',
'TYR': 'Y',
}
d_max = {}
d_ramachandran = {}
for res in d_residues.values():
d_ramachandran[res] = {}
for phi in range(-180, 180):
d_ramachandran[res][phi] = {}
for psi in range(-180, 180):
d_ramachandran[res][phi][psi] = 0
d_ramachandran = phipsi_comparison.parse_dihedrals(d_residues) ## slow
## d_ramachandran[res][phi][psi] = 1
for res in d_ramachandran.keys():
max = 0
for phi in d_ramachandran[res].keys():
for psi in d_ramachandran[res][phi].keys():
count = d_ramachandran[res][phi][psi]
if count > max:
max = count
d_max[res] = max
option = 'gromacs'
option = 'pdbs'
if option == 'frames':
l = range(50)
elif option == 'pdbs':
l = [
'150l',
]
chain = 'D'
elif option == 'gromacs':
l = []
for i in range(101):
l += ['2LZM_wt_trjconv_%i' % (i)]
chain = ' '
fd = open('2LZM_wt_trjconv_0.pdb', 'r')
lines = fd.readlines()
fd.close()
l_coords_ref = []
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
atom_name = line[12:16].strip()
if atom_name == 'CA':
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = numpy.array([
x,
y,
z,
])
l_coords_ref += [coord]
d_transformations = {}
for pdb in l:
if pdb == '2LZM_wt_trjconv_0.pdb':
continue
fd = open('%s.pdb' % (pdb), 'r')
lines = fd.readlines()
fd.close()
l_coords = []
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
atom_name = line[12:16].strip()
if atom_name == 'CA' and line[21] == chain:
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = numpy.array([
x,
y,
z,
])
l_coords += [coord]
l_coords_ref = l_coords_ref[:len(l_coords)]
rmsd = instance_geometry.superpose(l_coords_ref, l_coords)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
d_transformations[pdb] = [
tv1,
rm,
tv2,
]
for pdb in l:
print pdb
if option == 'gromacs':
## i = int(pdb[pdb.rindex('_')+1:])
prefix = 'rasmol%s' % (i)
else:
prefix = 'rasmol%s' % (pdb)
lines_rotated = []
## write rasmol script
lines_rasmol = [
'rasmol -nodisplay %s_rotated.pdb << EOF\n' % (pdb),
'cartoon\n',
'wireframe 0\n',
]
d_phipsi, lines_gnuplot = phipsi_plot.calculate_phipsi(pdb,
chain=chain)
fd = open('%s.pdb' % (pdb))
lines1 = fd.readlines()
fd.close()
for line1 in lines1:
record = line1[:6].strip()
if record in [
'HELIX',
'TURN',
'SHEET',
]:
lines_rotated += [line1]
if record != 'ATOM':
continue
if line1[21] != chain:
continue
atom_name = line1[12:16].strip()
## if atom_name != 'CA':
## continue
if atom_name not in [
'N',
'CA',
'C',
'O',
]:
continue
bfactor = float(line1[60:66])
res_no = int(line1[22:26])
res_name = line1[17:20].strip()
if res_no not in d_phipsi.keys():
bfactor = 50.
continue
else:
phi = int(d_phipsi[res_no][0])
psi = int(d_phipsi[res_no][1])
if phi == 180.:
phi = -180.
if psi == 180.:
psi = -180.
bfactor = (100 *
d_ramachandran[d_residues[res_name]][phi][psi] /
float(d_max[d_residues[res_name]]))
x = float(line1[30:38])
y = float(line1[38:46])
z = float(line1[46:54])
coordinate = numpy.array([
x,
y,
z,
])
if pdb != '2LZM_wt_trjconv_0':
tv1 = d_transformations[pdb][0]
rm = d_transformations[pdb][1]
tv2 = d_transformations[pdb][2]
coordinate = numpy.dot(coordinate - tv1, rm) + tv2
lines_rotated += [
'%s%8.3f%8.3f%8.3f%s%6.2f%s' %
(line1[:30], coordinate[0], coordinate[1], coordinate[2],
line1[54:60], bfactor, line1[66:])
]
h = 159. + 80 * bfactor / 100.
s = 240.
l = 120. + 120. * (50 - abs(bfactor - 50)) / 50.
r, g, b = hsl2rgb(
h,
s,
l,
)
lines_rasmol += [
'select %i\n' % (res_no),
'color [%i,%i,%i]\n' % (
r,
g,
b,
)
]
fd = open('%s_rotated.pdb' % (pdb), 'w')
fd.writelines(lines_rotated)
fd.close()
lines_rasmol += [
## 'ribbons\n',
'rotate x 100\n',
'rotate z 30\n',
'rotate x 100\n',
'rotate z 90\n',
'rotate x 40\n',
'rotate y -20\n',
'write %s.ppm\n' % (prefix),
'exit\n',
]
## write rasmol script to file
fd = open('%srasmol.src' % (prefix), 'w')
fd.writelines(lines_rasmol)
fd.close()
## execute rasmol script
os.system('source %srasmol.src > %srasmol.log' % (prefix, prefix))
## convert rasmol output
## os.system('convert %s.ppm -resize x80 %s.gif' %(prefix,prefix))
os.system('convert %s.ppm %s.gif' % (prefix, prefix))
## clean up
os.remove('%s.ppm' % (prefix))
os.remove('%srasmol.log' % (prefix))
os.remove('%srasmol.src' % (prefix))
## os.remove('frame%s.pdb' %(str(i).zfill(2)))
if option == 'gromacs':
line = 'convert '
for i in range(101): ## 0 to 100
line += 'rasmol%s.gif ' % (i)
for i in range(101 - 1 - 1, -1 + 1, -1): ## 99 to 1
line += 'rasmol%s.gif ' % (i)
line += '-loop 0 2lzm_MD.gif'
print line
os.system(line)
## for frame in range(50):
## os.remove('rasmol%s.gif' %(i))
return
def main():
## trjconv -f 2LZM_wt.trr -o 2LZM_wt_trjconv.pdb -s 2LZM_wt_MD.tpr -skip 10 -sep
fd = open('2lzm.pdb','r')
lines1 = fd.readlines()
fd.close()
lines2 = []
for line in lines1:
record = line[:6].strip()
if record in ['HELIX','TURN','SHEET',]:
lines2 += [line]
for i in range(50):
fd = open('%i.pdb' %(i),'r')
lines = fd.readlines()
fd.close()
lines = lines2+lines
fd = open('nma%i.pdb' %(i),'w')
fd.writelines(lines)
fd.close()
stop
import sys, os, numpy
sys.path.append('/home/people/tc/svn/tc_sandbox/quakes/')
import phipsi_comparison
sys.path.append('/home/people/tc/svn/tc_sandbox/misc/')
import phipsi_plot
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
d_residues = {
'ALA':'A','CYS':'C','ASP':'D','GLU':'E','PHE':'F',
'GLY':'G','HIS':'H','ILE':'I','LYS':'K','LEU':'L',
'MET':'M','ASN':'N','PRO':'P','GLN':'Q','ARG':'R',
'SER':'S','THR':'T','VAL':'V','TRP':'W','TYR':'Y',
}
d_max = {}
d_ramachandran = {}
for res in d_residues.values():
d_ramachandran[res] = {}
for phi in range(-180,180):
d_ramachandran[res][phi] = {}
for psi in range(-180,180):
d_ramachandran[res][phi][psi] = 0
d_ramachandran = phipsi_comparison.parse_dihedrals(d_residues) ## slow
## d_ramachandran[res][phi][psi] = 1
for res in d_ramachandran.keys():
max = 0
for phi in d_ramachandran[res].keys():
for psi in d_ramachandran[res][phi].keys():
count = d_ramachandran[res][phi][psi]
if count > max:
max = count
d_max[res] = max
option = 'gromacs'
option = 'pdbs'
if option == 'frames':
l = range(50)
elif option == 'pdbs':
l = ['150l',]
chain = 'D'
elif option == 'gromacs':
l = []
for i in range(101):
l += ['2LZM_wt_trjconv_%i' %(i)]
chain = ' '
fd = open('2LZM_wt_trjconv_0.pdb','r')
lines = fd.readlines()
fd.close()
l_coords_ref = []
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
atom_name = line[12:16].strip()
if atom_name == 'CA':
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = numpy.array([x,y,z,])
l_coords_ref += [coord]
d_transformations = {}
for pdb in l:
if pdb == '2LZM_wt_trjconv_0.pdb':
continue
fd = open('%s.pdb' %(pdb),'r')
lines = fd.readlines()
fd.close()
l_coords = []
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
atom_name = line[12:16].strip()
if atom_name == 'CA' and line[21] == chain:
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = numpy.array([x,y,z,])
l_coords += [coord]
l_coords_ref = l_coords_ref[:len(l_coords)]
rmsd = instance_geometry.superpose(l_coords_ref,l_coords)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
d_transformations[pdb] = [tv1,rm,tv2,]
for pdb in l:
print pdb
if option == 'gromacs':
## i = int(pdb[pdb.rindex('_')+1:])
prefix = 'rasmol%s' %(i)
else:
prefix = 'rasmol%s' %(pdb)
lines_rotated = []
## write rasmol script
lines_rasmol = [
'rasmol -nodisplay %s_rotated.pdb << EOF\n' %(pdb),
'cartoon\n',
'wireframe 0\n',
]
d_phipsi, lines_gnuplot = phipsi_plot.calculate_phipsi(pdb, chain = chain)
fd = open('%s.pdb' %(pdb))
lines1 = fd.readlines()
fd.close()
for line1 in lines1:
record = line1[:6].strip()
if record in ['HELIX','TURN','SHEET',]:
lines_rotated += [line1]
if record != 'ATOM':
continue
if line1[21] != chain:
continue
atom_name = line1[12:16].strip()
## if atom_name != 'CA':
## continue
if atom_name not in ['N','CA','C','O',]:
continue
bfactor = float(line1[60:66])
res_no = int(line1[22:26])
res_name = line1[17:20].strip()
if res_no not in d_phipsi.keys():
bfactor = 50.
continue
else:
phi = int(d_phipsi[res_no][0])
psi = int(d_phipsi[res_no][1])
if phi == 180.:
phi = -180.
if psi == 180.:
psi = -180.
bfactor = (
100
*d_ramachandran[d_residues[res_name]][phi][psi]
/float(d_max[d_residues[res_name]])
)
x = float(line1[30:38])
y = float(line1[38:46])
z = float(line1[46:54])
coordinate = numpy.array([x,y,z,])
if pdb != '2LZM_wt_trjconv_0':
tv1 = d_transformations[pdb][0]
rm = d_transformations[pdb][1]
tv2 = d_transformations[pdb][2]
coordinate = numpy.dot(coordinate-tv1,rm)+tv2
lines_rotated += ['%s%8.3f%8.3f%8.3f%s%6.2f%s' %(
line1[:30],
coordinate[0],coordinate[1],coordinate[2],
line1[54:60],bfactor,line1[66:]
)]
h = 159.+80*bfactor/100.
s = 240.
l = 120.+120.*(50-abs(bfactor-50))/50.
r,g,b = hsl2rgb(h,s,l,)
lines_rasmol += [
'select %i\n' %(res_no),
'color [%i,%i,%i]\n' %(
r, g, b,
)
]
fd = open('%s_rotated.pdb' %(pdb),'w')
fd.writelines(lines_rotated)
fd.close()
lines_rasmol += [
## 'ribbons\n',
'rotate x 100\n',
'rotate z 30\n',
'rotate x 100\n',
'rotate z 90\n',
'rotate x 40\n',
'rotate y -20\n',
'write %s.ppm\n' %(prefix),
'exit\n',
]
## write rasmol script to file
fd = open('%srasmol.src' %(prefix),'w')
fd.writelines(lines_rasmol)
fd.close()
## execute rasmol script
os.system('source %srasmol.src > %srasmol.log' %(prefix,prefix))
## convert rasmol output
## os.system('convert %s.ppm -resize x80 %s.gif' %(prefix,prefix))
os.system('convert %s.ppm %s.gif' %(prefix,prefix))
## clean up
os.remove('%s.ppm' %(prefix))
os.remove('%srasmol.log' %(prefix))
os.remove('%srasmol.src' %(prefix))
## os.remove('frame%s.pdb' %(str(i).zfill(2)))
if option == 'gromacs':
line = 'convert '
for i in range(101): ## 0 to 100
line += 'rasmol%s.gif ' %(i)
for i in range(101-1-1,-1+1,-1): ## 99 to 1
line += 'rasmol%s.gif ' %(i)
line += '-loop 0 2lzm_MD.gif'
print line
os.system(line)
## for frame in range(50):
## os.remove('rasmol%s.gif' %(i))
return
def morph(
self, eigenvectors_all_modes, nframes, chains, d_coordinates,
atoms_hessian, matrix_hessian, job,
):
'''This function puts in frames between the maximum amplitudes of a
movement given by eigenvectors. The values of the diagonal elements of the
hessian matrix are used for B factors to make coloring during simulation
possible.'''
sys.path.append('/home/people/tc/svn/tc_sandbox/quakes/')
import phipsi_comparison
sys.path.append('/home/people/tc/svn/tc_sandbox/misc/')
import phipsi
d_residues = {
'ALA':'A','CYS':'C','ASP':'D','GLU':'E','PHE':'F',
'GLY':'G','HIS':'H','ILE':'I','LYS':'K','LEU':'L',
'MET':'M','ASN':'N','PRO':'P','GLN':'Q','ARG':'R',
'SER':'S','THR':'T','VAL':'V','TRP':'W','TYR':'Y',
}
##d_ramachandran = phipsi_comparison.parse_dihedrals(d_residues)
d_ramachandran = {}
for res in d_residues.values():
d_ramachandran[res] = {}
for phi in range(-180,180):
d_ramachandran[res][phi] = {}
for psi in range(-180,180):
d_ramachandran[res][phi][psi] = 0
d_ramachandran = phipsi_comparison.parse_dihedrals(d_residues) ## slow
d_max = {}
for res in d_ramachandran.keys():
max = 0
for phi in d_ramachandran[res].keys():
for psi in d_ramachandran[res][phi].keys():
count = d_ramachandran[res][phi][psi]
if count > max:
max = count
d_max[res] = max
## print 'visualize the two extreme projections along a trajectory and interpolate n frames between them'
fd = open('/oxygenase_local/data/pdb/lz/pdb2lzm.ent','r')
lines = fd.readlines()
fd.close()
ss_lines = []
for line in lines:
record = line[:6].strip()
if record in ['HELIX','TURN','SHEET',]:
ss_lines += [line]
for mode in range(6,min(12,len(matrix_hessian))):
print mode
eigenvectors = eigenvectors_all_modes[mode]
## eigenvectors = length_adjustment(mode, eigenvectors)
output_vmd = ['REMARK color by connectivity (b-factor) or squared displacement (temperature factor)\n']
for frame in range(nframes):
lines_rasmol = [
'rasmol -nodisplay NMAframe%s.pdb << EOF\n' %(str(frame).zfill(2)),
'cartoon\n',
'wireframe 0\n',
]
prefix = 'NMA%s' %(frame)
## write rasmol script
lines = [
'rasmol -nodisplay NMAframe%s.pdb << EOF\n' %(str(frame).zfill(2)),
'cartoon\n',
'wireframe 0\n',
## 'ribbons\n',
## 'color temperature\n',
]
d_colors = {}
print mode,frame
output_rasmol = []
output_rasmol = list(ss_lines)
output_vmd.append('HEADER frame t= %4.3f\nMODEL 0\n' %(frame))
for chain in chains:
res_nos = d_coordinates['chains'][chain]['residues'].keys()
res_nos.sort()
for i_res_no in range(1,len(res_nos)-1):
res_no = res_nos[i_res_no]
for iCode in d_coordinates['chains'][chain]['residues'][res_no]['iCodes'].keys():
for altloc in d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'].keys():
res_name = d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['res_name']
## for atom_name in ['C','CA','N','O',]:
## for atom_name in d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms'].keys():
## if 'hessian' in d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms'][atom_name].keys():
C = d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms']['C']['coordinate']
CA = d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms']['CA']['coordinate']
N = d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms']['N']['coordinate']
O = d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms']['O']['coordinate']
vx_C = 64*eigenvectors[4*3*(i_res_no)+0]
vy_C = 64*eigenvectors[4*3*(i_res_no)+1]
vz_C = 64*eigenvectors[4*3*(i_res_no)+2]
vx_CA = 64*eigenvectors[4*3*(i_res_no)+3]
vy_CA = 64*eigenvectors[4*3*(i_res_no)+4]
vz_CA = 64*eigenvectors[4*3*(i_res_no)+5]
vx_N = 64*eigenvectors[4*3*(i_res_no)+6]
vy_N = 64*eigenvectors[4*3*(i_res_no)+7]
vz_N = 64*eigenvectors[4*3*(i_res_no)+8]
vx_O = 64*eigenvectors[4*3*(i_res_no)+9]
vy_O = 64*eigenvectors[4*3*(i_res_no)+10]
vz_O = 64*eigenvectors[4*3*(i_res_no)+11]
x2_C = C[0]+(1-2*float(frame)/float(nframes))*vx_C
y2_C = C[1]+(1-2*float(frame)/float(nframes))*vy_C
z2_C = C[2]+(1-2*float(frame)/float(nframes))*vz_C
x2_CA = CA[0]+(1-2*float(frame)/float(nframes))*vx_CA
y2_CA = CA[1]+(1-2*float(frame)/float(nframes))*vy_CA
z2_CA = CA[2]+(1-2*float(frame)/float(nframes))*vz_CA
x2_N = N[0]+(1-2*float(frame)/float(nframes))*vx_N
y2_N = N[1]+(1-2*float(frame)/float(nframes))*vy_N
z2_N = N[2]+(1-2*float(frame)/float(nframes))*vz_N
x2_O = O[0]+(1-2*float(frame)/float(nframes))*vx_O
y2_O = O[1]+(1-2*float(frame)/float(nframes))*vy_O
z2_O = O[2]+(1-2*float(frame)/float(nframes))*vz_O
C2 = [x2_C,y2_C,z2_C,]
CA2 = [x2_CA,y2_CA,z2_CA,]
N2 = [x2_N,y2_N,z2_N,]
O2 = [x2_O,y2_O,z2_O,]
C_prev = d_coordinates['chains'][chain]['residues'][res_no-1]['iCodes'][iCode]['altlocs'][altloc]['atoms']['C']['coordinate']
vx_C_prev = 64*eigenvectors[4*3*(i_res_no-1)+0]
vy_C_prev = 64*eigenvectors[4*3*(i_res_no-1)+1]
vz_C_prev = 64*eigenvectors[4*3*(i_res_no-1)+2]
x2_C_prev = C_prev[0]+(1-2*float(frame)/float(nframes))*vx_C_prev
y2_C_prev = C_prev[1]+(1-2*float(frame)/float(nframes))*vy_C_prev
z2_C_prev = C_prev[2]+(1-2*float(frame)/float(nframes))*vz_C_prev
C_prev2 = [x2_C_prev,y2_C_prev,z2_C_prev,]
phi = int(self.dihedral(C_prev2,N2,CA2,C2,))
N_next = d_coordinates['chains'][chain]['residues'][res_no+1]['iCodes'][iCode]['altlocs'][altloc]['atoms']['N']['coordinate']
vx_N_next = 64*eigenvectors[4*3*(i_res_no+1)+0]
vy_N_next = 64*eigenvectors[4*3*(i_res_no+1)+1]
vz_N_next = 64*eigenvectors[4*3*(i_res_no+1)+2]
x2_N_next = N_next[0]+(1-2*float(frame)/float(nframes))*vx_N_next
y2_N_next = N_next[1]+(1-2*float(frame)/float(nframes))*vy_N_next
z2_N_next = N_next[2]+(1-2*float(frame)/float(nframes))*vz_N_next
N_next2 = [x2_N_next,y2_N_next,z2_N_next,]
psi = int(self.dihedral(N2,CA2,C2,N_next2,))
bfactor = (
100
*d_ramachandran[d_residues[res_name]][phi][psi]
/float(d_max[d_residues[res_name]])
)
## index = int(100*bfactor/d_factors[mode][0])
##
## if index > 100 or index < 0:
## print index,bfactor
## stop
h = 159.+80*bfactor/100.
s = 240.
l = 120.+120.*(50-abs(bfactor-50))/50.
r,g,b = self.hsl2rgb(h,s,l,)
lines_rasmol += [
'select %i\n' %(res_no),
'color [%i,%i,%i]\n' %(
r, g, b,
)
]
line_out = 'ATOM %3s%s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f\n' %(
'C ', altloc, res_name, chain, int(res_no), iCode,
x2_C,y2_C,z2_C, bfactor, bfactor,
)
output_rasmol += [line_out]
line_out = 'ATOM %3s%s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f\n' %(
'CA ', altloc, res_name, chain, int(res_no), iCode,
x2_CA,y2_CA,z2_CA, bfactor, bfactor,
)
output_rasmol += [line_out]
line_out = 'ATOM %3s%s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f\n' %(
'N ', altloc, res_name, chain, int(res_no), iCode,
x2_N,y2_N,z2_N, bfactor, bfactor,
)
output_rasmol += [line_out]
line_out = 'ATOM %3s%s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f\n' %(
'O ', altloc, res_name, chain, int(res_no), iCode,
x2_O,y2_O,z2_O, bfactor, bfactor,
)
output_rasmol += [line_out]
fd = open('NMAframe%s.pdb' %(str(frame).zfill(2)),'w')
fd.writelines(output_rasmol)
fd.close()
output_vmd.append('TER\nENDMDL\n')
lines_rasmol += [
## 'ribbons\n',
'rotate x 100\n',
'rotate z 30\n',
'rotate x 100\n',
'rotate z 90\n',
'rotate x 40\n',
'rotate y -20\n',
'write %s.ppm\n' %(prefix),
'exit\n',
]
## write rasmol script to file
fd = open('%srasmol.src' %(prefix),'w')
fd.writelines(lines_rasmol)
fd.close()
## execute rasmol script
os.system('source %srasmol.src > %srasmol.log' %(prefix,prefix))
## convert rasmol output
## os.system('convert %s.ppm -resize x80 %s.gif' %(prefix,prefix))
os.system('convert %s.ppm %s.gif' %(prefix,prefix))
## clean up
os.remove('%s.ppm' %(prefix))
os.remove('%srasmol.log' %(prefix))
os.remove('%srasmol.src' %(prefix))
## os.remove('NMAframe%s.pdb' %(str(frame).zfill(2)))
line = 'convert '
for frame in range(50):
line += 'NMA%s.gif ' %(frame)
for frame in range(50-1-1,-1+1,-1):
line += 'NMA%s.gif ' %(frame)
line += '-loop 0 mode%s.gif' %(mode)
print line
os.system(line)
for frame in range(50):
os.remove('NMA%s.gif' %(frame))
fd = open(job+'_mode'+str(mode+1).zfill(2)+'.pdb', 'w') ## implicit path
fd.writelines(output_vmd)
fd.close()
return
