VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 02 2006 - 13:40:55 CDT

Hi,
  I assume that what you're asking is whether one can make movie
in which the representation changes over time as the movie progresses, yes?
The built-in movie types in the VMD movie maker don't change the active
representations. You can do this by making your own movie script
and using the user-defined movie type. Another way to do this is to
chain several shorter movies together.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 01, 2006 at 10:19:19PM -0400, Vyom Sharma wrote:
> Is it possible to make a movie out of different reps??
>
> Vyom
>
>
> On Jun 1, 2006, at 7:01 PM, John Stone wrote:
>
> >
> >Hi,
> > Did you send us the same sphere.pqr you loaded below? I'm not
> >getting
> >any of the bonding errors your message below was showing.
> >If you can upload the DX file to the VMD Public project area on
> >BioCoRE, I'd
> >like to have a look:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
> >
> >Most likely you just need to create an Isosurface representation after
> >the data is loaded. Also, although the APBS home page directs people
> >to use their my_functions.tcl script for loading DX files (in
> >particular
> >for older versions of VMD), the built-in DX reader plugin in VMD 1.8.4
> >is MUCH faster. (just load the DX file using the File menu as for
> >other
> >files...)
> >
> >To keep things simple to start with, try loading just the DX file into
> >VMD (using the built-in DX reader, rather than the load_pot script
> >routine..)
> >and see if you see the potential surface. Once you get that far, we
> >can
> >move on to the next questions..
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Jun 01, 2006 at 06:34:04PM -0400, Vyom Sharma wrote:
> >>I am getting a very strange problem for quite sometime now.
> >>I use a "PQR" file that i generate and run it on APBS to give me the
> >>potential data.
> >>VMD is able to show the molecule nicely but it is not able to
> >>visualize
> >>the potential data at all. Infact it does not show anything when I try
> >>to load the potential data.
> >>
> >>I am using the "my_functions" script to sort and load the potential
> >>data into VMD.
> >>Also I am attaching the "PQR" file (I can send the "pot.dx" file which
> >>contains the potential data , if required- its 27 MB big)
> >>
> >>While loading the potential using "load_pot" command, I get these
> >>messages:
> >>
> >>---------------------
> >>nfo) VMD for MACOSX, version 1.8.4 (April 17, 2006)
> >>Info) http://www.ks.uiuc.edu/Research/vmd/
> >>Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> >>Info) Please include this reference in published work using VMD:
> >>Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> >>Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> >>Info) -------------------------------------------------------------
> >>Info) Multithreading available, 1 CPU detected.
> >>Info) OpenGL renderer: ATI Radeon 9200 OpenGL Engine
> >>Info) Features: STENCIL MTX
> >>Info) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (6)
> >>vmd > source my_functions
> >>vmd > load_pot
> >>Info) Using plugin pdb for structure file sphere.pqr
> >>Info) Using plugin pdb for coordinates from file sphere.pqr
> >>Info) Determining bond structure from distance search ...
> >>ERROR) MolAtom 131: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 173: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 285: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 423: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 79: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 310: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 147: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 475: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 140: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 331: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 140: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 331: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 292: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 177: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 196: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 222: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 256: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 177: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 196: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 222: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 210: Exceeded maximum number of bonds (8).
> >>ERROR) MolAtom 110: Exceeded maximum number of bonds (8).
> >>ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps
> >>atom
> >>coordinates are in the wrong units?
> >>ERROR) BaseMolecule: Silencing bonding error messages.
> >>Info) Finished with coordinate file sphere.pqr.
> >>Info) Analyzing structure ...
> >>Info) Atoms: 501
> >>Info) Bonds: 1112
> >>Info) Residues: 53
> >>Info) Waters: 0
> >>---------------------------------------
> >>
> >>
> >>I would immensely appreciate any repsonse.
> >>
> >>Thanks
> >>Vyom
> >>
> >
> >
> >
> >>
> >
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078