VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Mar 24 2008 - 20:07:35 CDT

On Mon, 24 Mar 2008, Irene Newhouse wrote:

IN> Thank you! That's done the trick.

cool.

IN> Now I have another problem.... I'm trying to animate the resultant
IN> set of pdb files using animatepdbs.tcl from the scripts library. I
IN> can only animate the first 6 frames, because after that, there's a
IN> different number of waters & I get an "incorrect number of atoms"
IN> error message, and the frames are not loaded.

yep. that does not work.

IN> Is there a way to edit animatepdbs.tcl so that it can handle
IN> differing numbers of atoms from frame to frame?

this is not that easy, but there is help.

you can load each file into a new molecule, set up the visualization
for the first molecule, use the clone reps plugin to transfer it to
all others, and then use the multi-mol animate plugin...

http://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/

http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/

cheers,
   axel.

IN>
IN> Thanks yet again!
IN> Irene> Date: Mon, 24 Mar 2008 20:53:36 -0400> From: akohlmey_at_cmm.chem.upenn.edu> To: einew_at_hotmail.com> CC: vmd-l_at_ks.uiuc.edu> Subject: RE: vmd-l: script to read dcd frame-at-a-time & write a selection> > On Mon, 24 Mar 2008, Irene Newhouse wrote:> > IN> #initialize> IN> set numfr 350> IN> set pref h5a100> IN> set mymol [mol new parm7 $pref.prmtop]> > ok. this is not the correct syntax. see the docs.> you have to use:> > set mymol [mol new $pref.prmtop type parm7 waitfor all]> > this has the advantage of having a consistent syntax with> mol addfile...> > [...]> > IN> Thanks!> > > cheers,> axel.> > > -- > =======================================================================> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu> Center for Molecular Modeling -- University of Pennsylvania> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425> ===========================!
 ============================================> If you make something idiot-proof, the universe creates a better idiot.
IN> _________________________________________________________________
IN> Watch ?Cause Effect,? a show about real people making a real difference. Learn more.
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-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.