Henry, Sorry, I should have cut to the chase on what we're doing. The .txt file is a multi-frame molfile. Rather than rely on Jmol animation modes, we run it frame by frame ourselves. Cutting through my verbose specifics:
1) Load the animation file into Jmol. Note on the above: You're thinking computer generated molecular mechanics. I'm thinking Walt Disney making a movie! Aforementioned molfile is a frame by frame molfile construction acted out in Jmol. Same difference - a flip movie is a flip movie. 2) Do some set up stuff - i.e. set stage and get/set some important Jmol variables for the animation. 3) Run the animation frame by frame in a for loop - no auto animation. Run it just like Walt Disney did originally - flip, flip, flip... I know that this is the way Jmol does it with "animation," BUT... The reason that we do it this way is that in the loop we have complete control over every frame. We can skip frames. We can comment and draw in frames. We can freeze a frame and make Jmol do crazy things with it - then move on. We can stop, run some frames backwards, then move on. Etc. I hear you on user simplicity. The concept of animation templates written by someone who writes cleaner code that I do comes to mind. Actually, this particular animation was made by my friend Tom (not a scripter) from a template. All he had to mess with was the the stuff inside the loop, basically frame comments. I think the display * was a remnant from a previous animation he used as a template. He was doing some hide/show atoms in that previous animation. A funny thing happens when non-scripters play with this type of template: They love it! Tom went into an animation frenzy. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Feb 2, 2014, at 8:51 AM, Rzepa, Henry S <h.rz...@imperial.ac.uk> wrote: > Otis, > > Chlorination_of_anisoleF.TXT contains what? A gaussian log file? > > I think your script has 9 different start points, but they all proceed in a > positive direction from that point? > > I guess I want to re-order the frames in a Gaussian file, ie show 57 to 26, > then immediately jump to frame 1 and then show 1-25. This would involve > going backwards for the first sequence and forwards for the next. > > Actually, more importantly, I am trying to figure out how to get those > chemists who are not familiar with the type of script below not to be afraid > of trying. So I want to keep it as simple and generic as possible for them. > > I guess Bob may have to write code to implement eg frame 57-26,1-25; and > then run the animation in that order? > > > On 2 Feb 2014, at 13:01, Otis Rothenberger <osrot...@chemagic.com> wrote: > >> Henry, >> >> I'm not sure if this helps your situation, but we run animations in our own >> loop (e.g. below). You can pretty much do whatever you want with respect to >> frame display: >> >> var filePath = "animations/Chlorination_of_anisoleF.TXT"; >> var frameInterval = .1; >> load @filePath;hide *;background black;set echo top center;font echo 36 >> serif;color echo yellow;echo VMK Molecular Movies|Presents|Aromatic >> Clorination Reaction;delay 3; >> animation off;hover off;color label pink;select formalCharge <> 0;label >> %C;set echo top left;font echo 16 sansserif; >> color echo yellow;select *;var j = getProperty("modelInfo","modelCount"); >> for (var i = 1; i <= j; i++){ >> frame @i; >> if (i == 2){display *;echo Start with a bit of aluminum chloride.;delay >> 3;echo;} >> if (i == 3){display *;echo Add some dichlorine.;delay 3;echo;} >> if (i == 18){display *;echo Add anisole.;delay 3;echo;} >> if (i == 79){display *;echo A cyclohexadienyl cation intermediate;delay >> 3;echo;} >> if (i == 81){display *;echo A resonance contributor;delay 3;echo;} >> if (i == 86){display *;echo Another resonance contributor;delay 3;echo;} >> if (i == 93){display *;echo A 4th resonance contributor;delay 3;echo;} >> if (i == 159){display *;echo Loss of a proton, ;delay 3;echo;} >> if (i == 167){display *;echo regenerates the aromatic ring.;delay 3;} >> delay @{frameInterval}; >> } >> echo The final product is 1-chloro-4-methoxy-benzene.;delay 3;boundbox >> {*};centerat boundbox;zoom 0; >> >> Otis >> -- >> Otis Rothenberger >> o...@chemagic.com >> http://chemagic.com >> >> On Feb 2, 2014, at 3:57 AM, Rzepa, Henry S <h.rz...@imperial.ac.uk> wrote: >> >>> Has anybody solved this one? >>> >>> Gaussian computes an IRC by starting at the transition state (frame 1) >>> and following the IRC down to a rest in one direction (lets say frame 25), >>> then starting again from the geometry of frame 1 (this will now be >>> numbered 26) and computing the IRC in the other direction, down to say >>> frame 51. >>> >>> So to display a smooth IRC (one capable of palindromic reversal), one needs >>> to load the frames in the order: >>> >>> 51 > 27 > 1 > 25 (this avoids repeating 26, which is the same as 1). >>> >>> Unless I missed it, I do not think the frame command can be used to set >>> up this sequence? Can anyone enlighten me? >>> >>> I would point out that it is not unusual to compute IRCs with a total of >>> perhaps 400 frames, and loading and animating these frames is going to be >>> a tough ask of JSmol (and possibly Jmol as well). Perhaps one should not >>> try IRCs with so many frames at all? >>> ------------------------------------------------------------------------------ >>> WatchGuard Dimension instantly turns raw network data into actionable >>> security intelligence. It gives you real-time visual feedback on key >>> security issues and trends. Skip the complicated setup - simply import >>> a virtual appliance and go from zero to informed in seconds. >>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> ------------------------------------------------------------------------------ >> WatchGuard Dimension instantly turns raw network data into actionable >> security intelligence. It gives you real-time visual feedback on key >> security issues and trends. Skip the complicated setup - simply import >> a virtual appliance and go from zero to informed in seconds. >> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------------ > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
