Trusted, Bureaucrats
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<source lang="python">
# Start settings
reinitialize
bg_color white
set scene_buttons, 1
# Load protein and set name
load energy_1.pdb
prot='prot'
cmd.set_name("energy_1", prot)
# Load tensor pdb
load ./result_06_check_intermediate/final/tensor.pdb
#################################
# Scene 1 : Make default view
#################################
hide everything, prot
show_as cartoon, prot
zoom prot and polymer
scene F1, store, load of data, view=1
################################
# Scenes: We will go through the order like this
# 's2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex'
# s2: S2, the model-free generalised order parameter (S2 = S2f.S2s).
# s2f: S2f, the faster motion model-free generalised order parameter.
# s2s: S2s, the slower motion model-free generalised order parameter.
# amp_fast:
# amp_slow:
# te: Single motion effective internal correlation time (seconds).
# tf: Faster motion effective internal correlation time (seconds).
# ts: Slower motion effective internal correlation time (seconds).
# time_fast:
# time_slow:
# rex: Chemical exchange relaxation (sigma_ex = Rex / omega**2).
#modes = ['s2']
#modes = ['s2', 's2f']
modes = ['s2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex']
fdir = "./result_06_check_intermediate/final/pymol"
python
# File placement
if False:
for i, mode in enumerate(modes):
# Make name
protn = '%s_%s' % (prot, mode)
# Loop over file lines
fname = fdir + "/%s.pml"%mode
fname_out = fdir + "/0_mod_%s.pml"%mode
f_out = open(fname_out, "w")
with open(fname) as f:
for line in f:
line_cmd = ""
# Add to end of line, depending on command
if line[0] == "\n":
line_add = ""
elif line[0:4] == "hide":
line_add = " %s"%protn
# All not changed
elif line[0:8] == "bg_color":
line_add = ""
elif line[0:9] == "set_color":
line_add = ""
elif line[0:6] == "delete":
line_add = ""
else:
line_add = " and %s"%protn
# Modify line
line_cmd = line.strip() + line_add + "\n"
# Write the line
f_out.write(line_cmd)
f_out.close()
python end
# Make pymol objects
python
for i, mode in enumerate(modes):
protn = '%s_%s' % (prot, mode)
cmd.copy(protn, prot)
cmd.scene("F1")
cmd.disable(prot)
cmd.enable(protn)
cmd.scene("F%i"%(i+2), "store", mode, view=0)
python end
#################################
# Scenes
# #modes = ['s2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex']
scene F2
@./result_06_check_intermediate/final/pymol/0_mod_s2.pml
scene F2, store, s2, view=0
scene F3
@./result_06_check_intermediate/final/pymol/0_mod_s2f.pml
scene F3, store, s2f, view=0
#scene F4
#@./result_06_check_intermediate/final/pymol/0_mod_s2s.pml
#scene F4, store, s2s, view=0
</source>
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