Changes

Make a '''06_check_intermediate_pymol.pml ''' file, with this content.  {| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="python"># Start settingsreinitializebg_color whiteset scene_buttons, 1 # Load protein and set nameload energy_1.pdbprot='prot'cmd.set_name("energy_1", prot) # Load tensor pdbload ./result_06_check_intermediate/final/tensor.pdb ################################## Scene 1 : Make default view#################################hide everything, protshow_as cartoon, protzoom 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 placementif True: for i, mode in enumerate(modes)https: # 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 objectspythonfor 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@github.com/result_06_check_intermediatetlinnet/finalrelax_modelfree_scripts/pymolblob/0_mod_s2.pmlscene F2, store, s2: the model-free generalised order parameter (S2 = S2f.S2s), view=0 scene F3@.master/result_06_check_intermediate/final/pymol/0_mod_s2f06_check_intermediate_pymol.pmlscene F3, store, s2f: the faster motion model-free generalised order parameter, view=0 scene F4@./result_06_check_intermediate/final/pymol/0_mod_s2s06_check_intermediate_pymol.pmlscene F4, store, s2s: the slower motion model-free generalised order parameter, view=0 scene F5@./result_06_check_intermediate/final/pymol/0_mod_amp_fast.pmlscene F5, store, amp_fast, view=0 scene F6@./result_06_check_intermediate/final/pymol/0_mod_amp_slow.pmlscene F6, store, amp_slow, view=0 scene F7@./result_06_check_intermediate/final/pymol/0_mod_te.pmlscene F7, store, te: Single motion effective internal correlation time (seconds), view=0 scene F8@./result_06_check_intermediate/final/pymol/0_mod_tf.pmlscene F8, store, tf: Faster motion effective internal correlation time (seconds), view=0 scene F9@./result_06_check_intermediate/final/pymol/0_mod_ts.pmlscene F9, store, ts: Slower motion effective internal correlation time (seconds), view=0 scene F10@./result_06_check_intermediate/final/pymol/0_mod_time_fast.pmlscene F10, store, time_fast, view=0 scene F11@./result_06_check_intermediate/final/pymol/0_mod_time_slow.pmlscene F11, store, time_slow, view=0 scene F12@./result_06_check_intermediate/final/pymol/0_mod_rex.pmlscene F12, store, rex: Chemical exchange relaxation (sigma_ex = Rex / omega**2), view=0</source>|}]