Re: [Jmol-users] tying echoes to sets of frames

[Greg.Black <gre...@op...>]

Hi Otis,

This looks like a nice example using this really powerful feature of Jmol. Are you able to provide the multiframe file or a link to this animation on the web? I recently made a multiframe xyz file by scripting in Discovery Studio to illustrate protein torsion rotations. This animated well in JSmol, and is flexible and interactive, unlike a conventional 3D animation.

Cheers
Greg

________________________________________
From: Otis Rothenberger [osr...@ch...]
Sent: Saturday, May 17, 2014 4:34 AM
To: jmo...@li...
Subject: Re: [Jmol-users] tying echoes to sets of frames

Frieda,

If I responded with the idea before, forgive my aging memory.

A while back we wanted to do some animations where we had complete frame by frame control of the flow (echos, timing, atom display, etc). We settled on wrapping our multi frame file in a script loop of our own. The basic concept is very simple, and best illustrated with an example. I'll append a Diels/Alder animation loop script to this email.

You really have great control - echos anywhere, atoms leave and return to the "stage," delays, frame interval changes, you name it...

Otis

The script:


var filePath = "../animations/diels_alderF.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|A Diels-Alder 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 ==1) {var k = {model=i}.atomIndex.max + 1;var t = {model=i}.atomIndex.min;select within(branch, {atomIndex = k}, {atomIndex=t}); color cpk;hide selected;echo  2-methoxy-1,3-butadiene, an electron rich diene;delay 4;echo;}
if (i ==3) {var k = {model=i}.atomIndex.max + 1;var t = {model=i}.atomIndex.min;select within(branch, {atomIndex = k}, {atomIndex=t}); color cpk;hide selected;echo Rotation around the C2-C3 bond;delay 4;echo;}
if (i < 58) {var k = {model=i}.atomIndex.max + 1;var t = {model=i}.atomIndex.min;select within(branch, {atomIndex = k}, {atomIndex=t});   color cpk;hide  selected;}
if (i == 57){echo  generates this reactive conformation,;delay 4;echo;}
if (i == 58){display *;echo  ready to react with MVK, an electron poor dienophile;delay 4;echo;}
if (i == 58){display *;echo  once the two reactants are properly oriented.;delay 4;echo;}
if (i == 167){display *;echo  The pi systems align.;delay 3;echo;}
if (i == 190){display *;echo  They approach in parallel planes.;delay 4;echo;}
if (i == 233){display *;echo partial bonds all around;delay 4;echo;}

delay @{frameInterval};
}

echo The final product is this substituted cyclohexene. ;delay 3;boundbox {*};centerat boundbox;zoom 0;


--
Otis Rothenberger
ot...@ch...<mailto:ot...@ch...>
http://chemagic.com





On May 16, 2014, at 10:13 PM, Frieda Reichsman <fri...@ma...<mailto:fri...@ma...>> wrote:

Hi Bob et al.,

I would like an echo to appear at the top of the frame during frames 1-10 of an animation, then a different echo to appear in the same spot for frames 15-25, and a third for frames 30-35. I’ve been looking at 'set echo' in the script doc, where I see:
Echo text can be associated with a specific model, with visibility controlled by the frame<http://chemapps.stolaf.edu/jmol/docs/?ver=14.0#frame> command. See below.

and then below (as advertised)
set echo id MODEL (model number)

By default, when multiple models are present, all echo text is visible regardless of the model currently displayable using the frame<http://chemapps.stolaf.edu/jmol/docs/?ver=14.0#frame> command. The set echo ... MODEL command associates an echo with a specific model, allowing the text or image to appear and disappear when different models are displayed using the frame<http://chemapps.stolaf.edu/jmol/docs/?ver=14.0#frame> command.


I have tried many different permutations of this without success.  I am clearly misunderstanding something, possibly several things… Can someone point me in the right direction? What would a simple example command look like?

Frieda
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