From: lam nguyen (lamvn08_at_gmail.com)
Date: Tue Mar 13 2012 - 16:23:17 CDT

I found that the error does not appear if I start VMD with a DCD file
(together with a PSF) then use userdefined movie scripts. But if I
start VMD with a PDB file, I get the error when running userdefined
scripts. VMD does not change behavior if I delete the molecule and
load a new one whether the new file is DCD or PDB. So somehow the
start molecule file type dictates the VMD behavior.

Lam

On 3/12/12, lam nguyen <lamvn08_at_gmail.com> wrote:
> Hi John,
>
> I think I have VMD 1.9 and did not customize .vmdrc.
>
> Here is what I get:
>
> % package require vmdmovie
>
> 1.8
>
> % vmdinfo version
>
> 1.9
>
> % vmdinfo options
>
> LINUXAMD64 OPENGL FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA XINPUT LIBTACHYON
> VRPN NETCDF TCL PYTHON PTHREADS NUMPY SILENT
>
> Lam
>
> On Mon, Mar 12, 2012 at 1:53 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>>
>> Hi,
>> If you're still only running VMD 1.8.x, then yes, you will need
>> to update. On the other hand, another question I have for you is whether
>> you have customized anything in your .vmdrc or if you're running the
>> stock
>> VMD startup scripts? If you've customized it, you should make sure you
>> don't have any callbacks activated on things like the vmd_frame etc
>> before
>> you try to make a user-defined movie. We have been using the
>> user-defined
>> movie feature every day here recently, so it is working fine for us.
>>
>> What does this command say when you run it in the VMD console:
>> package require vmdmovie
>>
>> What does this command say when you run it in the VMD console:
>> vmdinfo version
>>
>> What does this command say when you run it in the VMD console:
>> vmdinfo options
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Sun, Mar 11, 2012 at 04:55:38PM -0700, lam nguyen wrote:
>> > Hi John,
>> > I got 1.8. I guess it's VMD version?
>> > Lam
>> >
>> > On Fri, Mar 9, 2012 at 6:45 PM, John Stone <johns_at_ks.uiuc.edu>
>> > wrote:
>> >
>> > Lam,
>> > What version of VMD are you running? What do you get if you
>> > run this command in the text console:
>> > package require vmdmovie
>> >
>> > Cheers,
>> > John Stone
>> > vmd_at_ks.uiuc.edu
>> > On Fri, Mar 09, 2012 at 05:57:53PM -0800, lam nguyen wrote:
>> > > Oh you're right Axel. I did not notice that I can choose none
>> when
>> > it asks
>> > > for svgalib. Now netpbm is installed. But the same error
>> > still
>> > persists
>> > > when I use usermovie.tcl.
>> > > Lam
>> > > On Fri, Mar 9, 2012 at 5:35 PM, Axel Kohlmeyer <
>> akohlmey_at_gmail.com>
>> > wrote:
>> > >
>> > > On Fri, Mar 9, 2012 at 7:34 PM, lam nguyen <
>> lamvn08_at_gmail.com>
>> > wrote:
>> > > > I tried to install netpbm again. It requires svgalib but
>> > I
>> > cannot get
>> > > > svgalib installed.
>> > >
>> > > no it doesn't. just compile netpbm without svgalib support.
>> > > it is unlikely that you'll ever need svgalib.
>> > >
>> > > axel.
>> > >
>> > > >
>> > > > Lam
>> > > >
>> > > >
>> > > > On Fri, Mar 9, 2012 at 3:31 PM, lam nguyen <
>> lamvn08_at_gmail.com>
>> > wrote:
>> > > >>
>> > > >> Hi John,
>> > > >>
>> > > >> Normal built-in movies are fine. Just tried them out.
>> Still
>> > cannot
>> > > use the
>> > > >> user-define on linux. :(
>> > > >>
>> > > >> Lam
>> > > >>
>> > > >>
>> > > >> On Fri, Mar 9, 2012 at 2:27 PM, John Stone <
>> johns_at_ks.uiuc.edu>
>> > wrote:
>> > > >>>
>> > > >>>
>> > > >>> Hi,
>> > > >>> Before you would be able to make any of the
>> > user-defined
>> > movies,
>> > > >>> you would need to ensure that the "normal" built-in
>> > movie
>> > types
>> > > >>> like the rocking movies work. If you don't have
>> > required
>> > tools like
>> > > >>> NetPBM installed, then there's no way that any of it is
>> going
>> > to
>> > > work
>> > > >>> correctly. I recommend you get that fixed first, and
>> once
>> > you get
>> > > the
>> > > >>> normal rocking movies running, the user-defined movies
>> should
>> > also
>> > > work.
>> > > >>>
>> > > >>> Cheers,
>> > > >>> John Stone
>> > > >>> vmd_at_ks.uiuc.edu
>> > > >>>
>> > > >>> On Fri, Mar 09, 2012 at 10:10:05AM -0800, lam nguyen
>> wrote:
>> > > >>> > Yes I did try those 2 scripts on linux and on
>> macbook.
>> > On linux
>> > > both
>> > > >>> > scripts did not work. On mac, one of them worked
>> fine,
>> > > >>> > the usermoviefade.tcl did not work.
>> > > >>> > If I recall correctly I might have failed
>> > installing
>> > netpbm on
>> > > linux
>> > > >>> > because I could not install all the dependencies.
>> Would
>> > that be
>> > > the
>> > > >>> > problem that gave the error? If yes I will try
>> install
>> > netpbm
>> > > again.
>> > > >>> > Thanks,
>> > > >>> > Lam
>> > > >>> >
>> > > >>> > On Thu, Mar 8, 2012 at 10:12 AM, John Stone
>> > <johns_at_ks.uiuc.edu>
>> > > >>> > wrote:
>> > > >>> >
>> > > >>> > Hi,
>> > > >>> > I'm not sure why you're having trouble there,
>> > it
>> > seems
>> > > >>> > reasonable.
>> > > >>> > Perhaps there's a typo in your script that I'm
>> > not
>> > seeing
>> > > below.
>> > > >>> > What happens if you download and run one of the
>> > example
>> > > >>> > user-defined
>> > > >>> > movie scripts that are posted here:
>> > > >>> >
>> http://www.ks.uiuc.edu/Research/vmd/plugins/vmdmovie/
>> > > >>> >
>> > > >>> >
>> > http://www.ks.uiuc.edu/Research/vmd/plugins/vmdmovie/usermovie.tcl
>> > > >>> >
>> > > >>> >
>> > >
>> >
>> http://www.ks.uiuc.edu/Research/vmd/plugins/vmdmovie/usermoviefade.tcl
>> > > >>> >
>> > > >>> > Cheers,
>> > > >>> > John Stone
>> > > >>> > vmd_at_ks.uiuc.edu
>> > > >>> > On Mon, Mar 05, 2012 at 10:49:00AM -0800, lam
>> nguyen
>> > wrote:
>> > > >>> > > Dear all,
>> > > >>> > > I want to learn how to make movies with
>> > user-defined
>> > > scripts.
>> > > >>> > I
>> > > >>> > started
>> > > >>> > > with a simple script from the VMD tutorial.
>> Here
>> > is the
>> > > >>> > content:
>> > > >>> > > proc moviecallback { args } {
>> > > >>> > > puts "User-defined movie frame update
>> callback
>> > frame:
>> > > >>> > > $::MovieMaker::userframe
>> > > >>> > > / $::MovieMaker::numframes"
>> > > >>> > > rotate y by 5
>> > > >>> > > }
>> > > >>> > > ## Easy-to-use proc to enable the
>> user-defined
>> > movie
>> > > frame
>> > > >>> > callback
>> > > >>> > > proc enablemoviecallback { } {
>> > > >>> > > trace add variable
>> > ::MovieMaker::userframe
>> > write
>> > > >>> > moviecallback
>> > > >>> > > }
>> > > >>> > > ## Easy-to-use proc to disable the
>> user-defined
>> > movie
>> > > frame
>> > > >>> > callback
>> > > >>> > > proc disablemoviecallback { } {
>> > > >>> > > trace remove variable
>> ::MovieMaker::userframe
>> > write
>> > > >>> > moviecallback
>> > > >>> > > }
>> > > >>> > > In the Tk console:
>> > > >>> > > source usermovie.tcl
>> > > >>> > > enablemoviecallback
>> > > >>> > > Then in the movie maker window I chose User
>> > defined
>> > > >>> > procedure.
>> > > >>> > > However I got an error message: Invalid
>> > input
>> > file
>> > > expansion
>> > > >>> > expression
>> > > >>> > > (no ']')
>> > > >>> > > Can anyone please tell me what I did wrong
>> here?
>> > > >>> > > Thanks
>> > > >>> > > Lam
>> > > >>> >
>> > > >>> > --
>> > > >>> > NIH Resource for Macromolecular Modeling and
>> > Bioinformatics
>> > > >>> > Beckman Institute for Advanced Science and
>> Technology
>> > > >>> > University of Illinois, 405 N. Mathews Ave,
>> Urbana, IL
>> > 61801
>> > > >>> > http://www.ks.uiuc.edu/~johns/ Phone:
>> > 217-244-3349
>> > > >>> > http://www.ks.uiuc.edu/Research/vmd/ 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
>> > > >>> http://www.ks.uiuc.edu/~johns/ Phone:
>> 217-244-3349
>> > > >>> http://www.ks.uiuc.edu/Research/vmd/ Fax:
>> 217-244-6078
>> > > >>
>> > > >>
>> > > >
>> > >
>> > > --
>> > > Dr. Axel Kohlmeyer
>> > > akohlmey_at_gmail.com http://goo.gl/1wk0
>> > >
>> > > College of Science and Technology
>> > > Temple University, Philadelphia PA, USA.
>> >
>> > --
>> > NIH Resource for Macromolecular Modeling and Bioinformatics
>> > Beckman Institute for Advanced Science and Technology
>> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> > http://www.ks.uiuc.edu/Research/vmd/ 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
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>>
>