Re: [PyMOL] pymol movie scripting for beginners questions
Hi Aiko, That's impressive for only using PyMOL one day. As a solution, just add, mview reinterpolate right before frame 433. So, at the end of your file you should have: frame 432 set_view (\ 0.264227241,0.815219104,0.515365601,\ -0.842250228, -0.065306552,0.535127521,\ 0.469904959, -0.575454950,0.669362724,\ 0.0,0.0, -152.198883057,\ 47.851242065, 41.281734467, 31.806066513,\ 112.558006287, 191.839767456, -20.0 ) mview store, object=TOP mview store, object=BOTTOM mview store mview interpolate, object=TOP mview interpolate, object=BOTTOM mview reinterpolate frame 433 mplay By the way, if you use scenes (http://www.pymolwiki.org/index.php/Scene), you may find that moviemaking in PyMOL becomes much easier. Cheers, -- Jason On Fri, Feb 11, 2011 at 5:52 AM, Aiko Matsumoto aikomatsumoto1...@googlemail.com wrote: 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,\ 0.0, 0.0, -235.838287354,\ 48.424118042, 41.582153320, 30.356651306,\ 185.936691284, 285.739868164, -20.0 ) 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,\ 0.0, 0.0, -152.198883057,\ 47.851242065, 41.281734467, 31.806066513,\ 112.558006287, 191.839767456, -20.0 ) 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
[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,\ 0.0,0.0, -235.838287354,\ 48.424118042, 41.582153320, 30.356651306,\ 185.936691284, 285.739868164, -20.0 ) 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,\ 0.0,0.0, -152.198883057,\ 47.851242065, 41.281734467, 31.806066513,\ 112.558006287, 191.839767456, -20.0 ) 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 -- 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 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol movie scripting for beginners questions
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,\ 0.0,0.0, -235.838287354,\ 48.424118042, 41.582153320, 30.356651306,\ 185.936691284, 285.739868164, -20.0 ) 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,\ 0.0,0.0, -152.198883057,\ 47.851242065, 41.281734467, 31.806066513,\ 112.558006287, 191.839767456, -20.0 ) 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 --- --- 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
