VMD-L Mailing List

From: Emmanuel, Alaina (A.E.Emmanuel_at_warwick.ac.uk)
Date: Fri Nov 28 2014 - 10:58:51 CST

This is really great news, and not to mention, perfect timing!
Thank you so much for all your hard work. This is exactly something that I've looked for in VMD.

My only suggestion would be the following:
For new vmd users it might also be useful to include a specific example with a protein.pdb file. I know that it helped me a lot. In the (lovely) youtube video, you have shown a molecule that you loaded. Maybe it it could serve as a good reference or comparison to test that we fully understand the code. This way we know exactly how to apply the exampleREMD.tcl<http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/userani/exampleREMD.tcl> . It's just a small suggestion, but hopefully it will help a lot. Below is an example where you have already done this for the usermoviefade.tcl file ( http://www.ks.uiuc.edu/Research/vmd/plugins/vmdmovie/usermoviefade.tcl ), except in our case we may have an additional xtc file:

## setup for making the movie

proc setupmovie { } {
  mol delete all
  mol new 1ap9

  material add Fade copy Transparent
  mol modstyle 0 0 VDW 1.000000 8.000000
  mol modmaterial 0 0 Fade

  enablemoviecallback

  after idle { puts "Don't forget to set movie type to user-defined in the Movie Settings" }
}

Best wishes,

Alaina

From: Norman Geist <norman.geist_at_uni-greifswald.de<mailto:norman.geist_at_uni-greifswald.de>>
Date: Friday, 28 November 2014 07:04
To: "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>" <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: vmd-l: Announcement: User defined movie animation

For everybody who's interested and also to make this searchable on the web, I'm announcing a new easy-to-use user defined movie animation
system for VMD for use with the standard Movie Maker and the "user defined procedure".

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/userani/

To use it one doesn't need to be good in TCL programming, it's simply writing some kind of storyboard, see example usage and FAQ. But who knows TCL can even extend it quite easy.
Currently is has animation procedures prepared for:

- Rotation (real and graphically)

- Translation (real and graphically)

- AutoZoom to All/Mol/Rep

- AutoFocus to All/Mol/Rep

- Transparency fading

Animations can easily happen in parallel. Also any TCL procedure or command can be used, including all VMD commands.
The system has visualization routines to show what has been configured:

Info) Storyboard: (ordered like added)
kickoff material {change opacity Goodsell 1.000000}
kickoff material {change opacity Edgy 1.000000}
kickoff mol {showrep 0 1 1}
kickoff mol {showrep 0 2 0}
kickoff display resetview
test AutoFocusAllVisible {}
test AutoScaleAllVisible {}
test rotate {x 360}
test FadeTransparency {Goodsell 1 0}
test2 mol {showrep 0 1 0}
test2 mol {showrep 0 2 1}
test3 FadeTransparency {Goodsell 0 0.5}
test3 AutoFocusAllVisible {}
test3 AutoScaleAllVisible {}
test4 FadeTransparency {Goodsell 0.5 0}
test4 FadeTransparency {Edgy 1 0}
test5 AutoScaleMolRepVisible {0 3}
test5 AutoFocusMolRepVisible {0 3}
test6 AutoScaleMolRepVisible {0 3}
test6 AutoFocusMolRepVisible {0 3}
test6 rotate {x 90}

Info) Timeline: (* = freeze)
                      0 48 96 144 192 240 288 336 384 432 480
                      |______|______|______|______|______|______|______|______|______|______|
kickoff [ 0 1 10] |>
   test [ 0 1 192] |***************************>
  test2 [192 1 193] |>
  test3 [192 1 240] |------>
  test4 [240 1 288] |------>
  test5 [288 1 432] |********************>
  test6 [432 1 480] |------>
                      |______|______|______|______|______|______|______|______|______|______|
                      0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
                      0s 2s 4s 6s 8s 10s 12s 14s 16s 18s 20s

This is a early example video: http://www.youtube.com/watch?v=Qa0ZmtRTSpM

Let me know your opinions or questions

 - Norman Geist -