Dear Mailing list!
I have just started using pymol to make a molecular movie of a protein
ligand system.
What I came up with is:
###########################################################################
reinitialize
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
set static_singletons, off
set movie_auto_interpolate, off
set movie_loop, off
config_mouse three_button_motions, 1
set movie_fps, 30
bg_color white
load 2fpt-complex-aligned.pdb
hide everything, all
create ligand, resn ILB and resi 405
create cofactor, resn FMN and resi 398
create substrate, resn ORO and resi 399
create site2, (cofactor substrate)
create Nterm, (not resn HOH and resi 30-77)
create Cterm, (not resn HOH and resi 78-396)
create water1, byres resn HOH within 8 of ligand
create water2, byres resn HOH within 8 of site2
create pocket1, byres all within 7 of ligand and not resn HOH
create pocket2, byres all within 7 of site2 and not resn HOH
create TOP, Cterm site2
create BOTTOM, Nterm
create BOTH, TOP BOTTOM
show cartoon, TOP BOTTOM
show sticks, ligand
show sticks, (TOP and (resn FMN or resn ORO))
#show nb_spheres, water1
#show nb_spheres, water2
color meitnerium, ss h
color titanium, ss l
color thorium, ss s
util.cbay ligand
util.cbay (TOP and (resn FMN or resn ORO))
#spectrum b, blue_white_red, water1
#spectrum b, blue_white_red, water2
set_view (\
0.296377361, 0.815219104, 0.497568905,\
-0.806614339, -0.065306552, 0.587461531,\
0.511405945, -0.575454950, 0.638211489,\
0.000000000, 0.000000000, -235.838287354,\
48.424118042, 41.582153320, 30.356651306,\
185.936691284, 285.739868164, -20.000000000 )
mset 1 x433
frame 1
mview store, object=TOP
mview store, object=BOTTOM
mview store
frame 180
translate [0,10,0], object=TOP
translate [0,-10,0], object=BOTTOM
mview store, object=TOP
mview store, object=BOTTOM
mview store
mview interpolate, object=TOP
mview interpolate, object=BOTTOM
frame 282
util.mroll(180,282,360)
mview store, object=TOP
mview store, object=BOTTOM
mview store
frame 382
translate [0,-10,0], object=TOP
translate [0,10,0], object=BOTTOM
util.mroll(282,382,360)
mview store, object=TOP
mview store, object=BOTTOM
mview store
mview interpolate, object=TOP
mview interpolate, object=BOTTOM
frame 432
set_view (\
0.264227241, 0.815219104, 0.515365601,\
-0.842250228, -0.065306552, 0.535127521,\
0.469904959, -0.575454950, 0.669362724,\
0.000000000, 0.000000000, -152.198883057,\
47.851242065, 41.281734467, 31.806066513,\
112.558006287, 191.839767456, -20.000000000 )
mview store, object=TOP
mview store, object=BOTTOM
mview store
mview interpolate, object=TOP
mview interpolate, object=BOTTOM
frame 433
mplay
##########################################################################################
I am just beginning to gain familiarity with this but probably someone
can point me into the right direction?
My problem is that if I use the script in exactly the way I posted above
then I don't get the change view (frame 382 to 432).
At the end the 'set view' just shows up without any interpolation.
However, when I use a "mview reinterpolate" statement at the end of the
script,
then frame 382 to 432 essentially zoom into the binding pocket, which is
what I want BUT suddenly all attempts to rotate the system (frames 180
to 280 and 280 to 380) have somehow been disabled, apart from 2 little
rocking motions at exactly 2 frames, though I do get the translation right.
After day one in using pymol I might not be the expert but even
following several examples online (pymol-wiki and such) don't really
give me any indication
as to what is going on as there doesn't seem to be a really complex
movie that allows the study on frames/states plus scenes plus proper
complex use of mdo in one and the same example movie.
Please please help, I am getting desperate here!
Thanks
Aiko
PhD student
Uni Bristol
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