From: Harry M. G. <Har...@we...> - 2010-03-09 08:05:41
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BS"D Dear All, I would like to create a movie (for a course) showing how a molecule undergoes crystallographic symmetry operations. So, for example, if looking at a 2-fold screw axis, the movie would show either: 1. The molecule rotating about the 2-fold, then translating 1/2 a unit cell (in either order) 2. Or, the molecule undergoing a screw transformation (combined rotation and translation). So one would generate about 50 (or less?) intermediate structures, each one transformed a successive fraction of the desired operation. It seems that SuperSym will generate the symmetry mates, but I want to animate how you go from one to the next. Is there a facility that someone has already created? Thanks Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology har...@we... Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel |
From: Jason V. <jas...@sc...> - 2010-03-12 06:16:43
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Harry, Here's how I would do it. Load the original object. Create a duplicate of it. Next, create your symmetry mates. Align the duplicate to the symmetry mate of choice. Create a blank movie (eg. mset 1x120, or Movie > Append > 4 Seconds). Now, store the original object's position at frame 1. Then at frame 60 issue: "matrix_copy duplicate, original", and store original's new position. Let me know if that works for you. Cheers, -- Jason On Tue, Mar 9, 2010 at 2:33 AM, Harry M. Greenblatt <Har...@we...> wrote: > BS"D > Dear All, > I would like to create a movie (for a course) showing how a molecule > undergoes crystallographic symmetry operations. So, for example, if looking > at a 2-fold screw axis, the movie would show either: > 1. The molecule rotating about the 2-fold, then translating 1/2 a unit > cell (in either order) > 2. Or, the molecule undergoing a screw transformation (combined rotation > and translation). > So one would generate about 50 (or less?) intermediate structures, each one > transformed a successive fraction of the desired operation. > It seems that SuperSym will generate the symmetry mates, but I want to > animate how you go from one to the next. Is there a facility that someone > has already created? > Thanks > Harry > > > > > ------------------------------------------------------------------------- > > Harry M. Greenblatt > > Associate Staff Scientist > > Dept of Structural Biology har...@we... > > Weizmann Institute of Science Phone: 972-8-934-3625 > > Rehovot, 76100 Facsimile: 972-8-934-4159 > > Israel > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Jason V. <jas...@sc...> - 2010-03-23 00:17:54
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On Mon, Mar 22, 2010 at 4:27 AM, Harry M. Greenblatt <Har...@we...> wrote: > BS"D > Dear Jason, > I have tried to implement what you suggested, but seeing as I haven't > made a movie in PyMOL in a long time (and was never very expert at it), I > don't seem to have got it working. Here is what I did, on my Mac (10.4.11), > with PyMOL 1.1r1 > I loaded 1yme, which has space group P21. > I then duplicated it from the Actions menu, and got obj01. > I then generated symmetry mates within 4 A of 1yme, and displayed only > 1yme_01000100 since this shows the 2 fold screw axis along b. > Again, from the actions menu, for obj01 I did Align > To Molecule > > 1yme_01000100. > Then I issued the command "mset 1 x120" > followed by: > mview store, 1, object=1yme > frame 60 > matrix_copy obj01, 1yme > mview store, 60, object=1yme > I then clicked on play. The movie ran through the 120 frames, but nothing > happened on the screen. > So, what did I do wrong? > Thanks > Harry Harry, I forgot the "matrix_mode" option. Here's a script that should get your first simple movie done for 1yme and help you with others. # fetch a protein with a great name fetch 1yme, one, async=0 # symmetry expand symexp foo, one, one, 4 # rename for easier use; call it "two" set_name foo01-100-1,two # remove others dele foo* # setup the camera view orient # set up a simple movie and save camera position mset 1x60 mview store # save mobile objects original position mview store, object=one # align the two objects align one, two, object=aln # grab the transformation matrix mm = cmd.get_object_matrix("one") # undo the transformation matrix_reset one frame 60 # this caused the problems set matrix_mode, 2 # move object one cmd.transform_object("one", mm) # store its new position which # PyMOL automaticaly reinterpolates for us mview store, object=one mplay Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Harry M. G. <Har...@we...> - 2010-03-23 09:51:26
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BS"D Dear Jason, Thank you for your time. I followed your script, and under PyMOL 1.2 was able to animate the transformation from (x,y,z) to (-x, y + 1/2, -z). After watching the movie several times, however, I got the impression that something was wrong. So I displayed the unit cell of both the starting molecule and the transformed one. In theory, this transformation should not cause any rotational motion to atoms on the b axis; they should only show translational motion. Likewise, the b axis of the drawn unit cell should remain co-linear with the target unit cell b axis. Unfortunately, while PyMOL is interpolating *a* transformation between the two molecules, it is not the crystallographic one, since the b axis clearly undergoes "lateral" movement. I have attached two pictures; one at the "start", and one just past the midpoint, showing this deviation in the position of the b axis. The blue sphere is an atom that is very close to the b axis. The green molecule is the animated one. I'm not sure whether this is a bug or just the way PyMOL interpolates, but I'm afraid it's not quite what I was looking for. Thanks for your efforts, Harry  > > I forgot the "matrix_mode" option. Here's a script that should get > your first simple movie done for 1yme and help you with others. > ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology har...@we... Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel |
From: Jason V. <jas...@sc...> - 2010-03-20 15:33:44
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Felix, It's currently not easy, but I could modify the symexp command (or create another) to take fractional parameters. I'll put that on the list of things to do. Thanks, -- Jason On Fri, Mar 12, 2010 at 2:58 AM, Felix Frolow <mbf...@po...> wrote: > Jason > Another request related to symmetry. > It will be useful for some to be able to create set of symmetry related molecules > in a box defined by fractional coordinates > Example: if one need to exhibit packing in a cell of 40, 60, 700 Angstrom (could be a real case, we have one such system, in work), it is not as easy as exhibiting packing in a cell of 250, 250, 250 Angstrom. > Could it be done? > Dr Felix Frolow > Professor of Structural Biology and Biotechnology > Department of Molecular Microbiology > and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallographica D, co-editor > > e-mail: mbf...@po... > Tel: ++972 3640 8723 > Fax: ++972 3640 9407 > Cellular: ++972 547 459 608 > > On Mar 12, 2010, at 08:16 , Jason Vertrees wrote: > >> Harry, >> >> Here's how I would do it. Load the original object. Create a >> duplicate of it. Next, create your symmetry mates. Align the >> duplicate to the symmetry mate of choice. Create a blank movie (eg. >> mset 1x120, or Movie > Append > 4 Seconds). Now, store the original >> object's position at frame 1. Then at frame 60 issue: "matrix_copy >> duplicate, original", and store original's new position. >> >> Let me know if that works for you. >> >> Cheers, >> >> -- Jason >> >> >> >> On Tue, Mar 9, 2010 at 2:33 AM, Harry M. Greenblatt >> <Har...@we...> wrote: >>> BS"D >>> Dear All, >>> I would like to create a movie (for a course) showing how a molecule >>> undergoes crystallographic symmetry operations. So, for example, if looking >>> at a 2-fold screw axis, the movie would show either: >>> 1. The molecule rotating about the 2-fold, then translating 1/2 a unit >>> cell (in either order) >>> 2. Or, the molecule undergoing a screw transformation (combined rotation >>> and translation). >>> So one would generate about 50 (or less?) intermediate structures, each one >>> transformed a successive fraction of the desired operation. >>> It seems that SuperSym will generate the symmetry mates, but I want to >>> animate how you go from one to the next. Is there a facility that someone >>> has already created? >>> Thanks >>> Harry >>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> >>> Harry M. Greenblatt >>> >>> Associate Staff Scientist >>> >>> Dept of Structural Biology har...@we... >>> >>> Weizmann Institute of Science Phone: 972-8-934-3625 >>> >>> Rehovot, 76100 Facsimile: 972-8-934-4159 >>> >>> Israel >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |