Aiko,
I can't directly comment on your problem, but I had good experience with
the eMovie plugin. May be give that a try.
http://www.weizmann.ac.il/ISPC/eMovie.html
HTH
Carsten
> -----Original Message-----
> From: Aiko Matsumoto [mailto:aikomatsumoto1...@googlemail.com]
> Sent: Friday, February 11, 2011 5:52 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] pymol movie scripting for beginners questions
>
> 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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The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
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