Re: [Jmol-users] FW: Animating Z transformations
move has the slab parameter, but does not take a time. moveto doesn't take slab The for loop that Bob has suggested will be your best choice -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] FW: Animating Z transformations
some suggestions...
On Fri, Nov 12, 2010 at 5:41 AM, Matthew Saderholm <
matthew_saderh...@berea.edu> wrote:
> Greetings,
>
> I am sure that I am missing something, but I can't get a particular
> animation script to work. I want to do the following set of steps:
>
>
> 1. load the iconic DNA transcription factor structure (1d66)
> 2. rotate it to align the helix along the Z axis (in/out of screen)
> 3. color & spacefill the atoms by structure
> 4. turn on slab
> 5. translate the structure along the Z axis so that the front edge of the
> molecule is slowly clipped off, showing the spiraling DNA strands and bound
> protein.
>
> I can get my script to visually do everything but clip off the front. I
> thought that using a command like this would do the trick:
>
> reset; move 0 0 90 0 0 0 0 0 0.5; move 0 60 0 0 0 0 0 0 0.5; move 0 0 180 0
> 0 0 0 0 0.5;
> (rotates structure to line up on Z axis)
>
> select all; color chain; delay .1; wireframe 30; spacefill 30; delay .1;
> spacefill 50; delay .1; spacefill 75; delay .1; spacefill 100; delay .1;
> spacefill 125; delay .1; spacefill 150; delay .1; spacefill 175; delay .1;
> spacefill 200; delay .1; spacefill 225; delay .1; spacefill 250; delay .1;
> spacefill 275; delay .1; spacefill 300; delay .1; spacefill 325; delay .1;
> spacefill 350; delay .1; spacefill 375; delay .1; spacefill 400; delay .1;
> spacefill;
> (animates the structure to go up to spacefill from wireframe)
>
>
for (var i = 30; i <= 400; i+= 5) { spacefill @i; delay .1 }
lets you adjust it more easily
slab on; slab 100;
> (I think this is the correct setting)
>
> move 0 0 0 0 0 0 100 0 5
> (does not work, or at least I don't see any change)
>
The script as written works nicely up to when it is is supposed to slowly
> slice off the structure. I can manually slab through the molecule at this
> point, so I am pretty sure there should be a way to put this into a script.
> It sure seems like a simple Z translation is all that is called for, but I
> can't get a "move" or a "translate z" to make any difference. I hope I am
> just overlooking something obvious. If anyone can help figure out how, I'd
> appreciate it.
>
>
You might try just animating the slab:
for (var i = 100; i >= 0; i-=5) { slab @i; delay .1 }
Bob
Thanks,
>
> Matt
> --
> Matthew J. Saderholm
> Associate Professor of Chemistry
> Berea College,
> Berea, KY 40404
> 859-985-3322
>
>
>
>
>
> --
> Centralized Desktop Delivery: Dell and VMware Reference Architecture
> Simplifying enterprise desktop deployment and management using
> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
> client virtualization framework. Read more!
> http://p.sf.net/sfu/dell-eql-dev2dev
> ___
> Jmol-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Centralized Desktop Delivery: Dell and VMware Reference Architecture
Simplifying enterprise desktop deployment and management using
Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
client virtualization framework. Read more!
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Re: [Jmol-users] FW: Animating Z transformations
Thanks Angel, I put in slab 90; delay 0.1; slab 80; delay 0.1; slab 70; delay 0.1; slab 60; delay 0.1; slab 50; delay 0.1; slab 40; delay 0.1; slab 30; delay 0.1; slab 20; delay 0.1; slab 10; delay 0.1; slab 0; and that did the trick. Is there a way to do this with the move or moveto command? What I used does seem to be more brute force than elegant. Matt -- Matthew J. Saderholm Associate Professor of Chemistry Berea College Berea, KY 40404 859-985-3322 From: Angel Herráez [angel.herr...@uah.es] Sent: Friday, November 12, 2010 7:15 AM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] FW: Animating Z transformations (I was probably wrong when I said that Z translation and zoom are the same, but the main point still applies) -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] FW: Animating Z transformations
(I was probably wrong when I said that Z translation and zoom are the same, but the main point still applies) -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] FW: Animating Z transformations
Hi Matt I'm not sure of this, but rather than changing the Z translation I would try changing the slab incrementally When you say that it works manually using the mouse, are you zooming in? That is what Z translation means. Or are you shifting the slab plane? That is waht an incrmemental slab command will do -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] FW: Animating Z transformations
Greetings, I am sure that I am missing something, but I can't get a particular animation script to work. I want to do the following set of steps: 1. load the iconic DNA transcription factor structure (1d66) 2. rotate it to align the helix along the Z axis (in/out of screen) 3. color & spacefill the atoms by structure 4. turn on slab 5. translate the structure along the Z axis so that the front edge of the molecule is slowly clipped off, showing the spiraling DNA strands and bound protein. I can get my script to visually do everything but clip off the front. I thought that using a command like this would do the trick: reset; move 0 0 90 0 0 0 0 0 0.5; move 0 60 0 0 0 0 0 0 0.5; move 0 0 180 0 0 0 0 0 0.5; (rotates structure to line up on Z axis) select all; color chain; delay .1; wireframe 30; spacefill 30; delay .1; spacefill 50; delay .1; spacefill 75; delay .1; spacefill 100; delay .1; spacefill 125; delay .1; spacefill 150; delay .1; spacefill 175; delay .1; spacefill 200; delay .1; spacefill 225; delay .1; spacefill 250; delay .1; spacefill 275; delay .1; spacefill 300; delay .1; spacefill 325; delay .1; spacefill 350; delay .1; spacefill 375; delay .1; spacefill 400; delay .1; spacefill; (animates the structure to go up to spacefill from wireframe) slab on; slab 100; (I think this is the correct setting) move 0 0 0 0 0 0 100 0 5 (does not work, or at least I don't see any change) The script as written works nicely up to when it is is supposed to slowly slice off the structure. I can manually slab through the molecule at this point, so I am pretty sure there should be a way to put this into a script. It sure seems like a simple Z translation is all that is called for, but I can't get a "move" or a "translate z" to make any difference. I hope I am just overlooking something obvious. If anyone can help figure out how, I'd appreciate it. Thanks, Matt -- Matthew J. Saderholm Associate Professor of Chemistry Berea College, Berea, KY 40404 859-985-3322 -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
