From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 22 2004 - 11:45:35 CST

Cosmin,
  Thanks for the note about the User's guide, I'll make sure that
gets fixed for the next version. Let us know if you spot any other
things missing like that.

  John

On Mon, Mar 22, 2004 at 06:56:03PM +0100, Cosmin ROMAN wrote:
> Thanks John,
>
> I blindly figured it out yesterday. You know, the "user" field in the
> "atomselect" is not referenced in the user's guide, I had to guess it (and
> look into vmd's code). Otherwise, it is very strange, my script looks very
> much like yours except for the "fake trajectory" where I used a loop over
> "animate dup frame 0 0"
>
> A powerful feature this User color is ...
>
> Thank you again,
> Cosmin
>
>
> :*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:
> :
> Cosmin ROMAN, Ph.D. Student.
> :
> TIMA-INPG, MNS Group,
> : 46 Avenue Félix Viallet,
> 38031 Grenoble Cedex, FRANCE.
> :
> Tel : 00 33 4 76 57 48 34
> : Fax : 00 33 4 76 47 38 14
> e-mail : cosmin.roman_at_imag.fr
> :
> :*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:
> ----- Original Message -----
> From: "John Stone" <johns_at_ks.uiuc.edu>
> To: "Cosmin ROMAN" <cosmin.roman_at_imag.fr>
> Cc: <vmd-l_at_ks.uiuc.edu>
> Sent: Monday, March 22, 2004 6:18 PM
> Subject: Re: vmd-l: coloring method User
>
>
> > Hi,
> > I've included a simple Tcl script that illustrates how one would set
> > the values of the "User" color field to animate something. Let me know
> > if you need more examples/info on this. Basically, the "User" color field
> > is a time-varying field (unlike all the others) and at present the only
> way
> > to get data there is to put it there with your own script (i.e. none of
> the
> > plugins read data for the "User" field presently).
> >
> > Enjoy,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > ##
> > ## Example script that sets the "User" data field with time varying values
> > ## which can be used to color over time
> > ##
> >
> > ##
> > ## load a fake "trajectory" by repeatedly loading the same PDB :-)
> > ##
> > set file /Home/h2/johns/vmd/proteins/brH.pdb
> > if {[molinfo num] > 0} {
> > mol delete all
> > }
> > mol new $file
> > for {set i 0} {$i<20} {incr i} {
> > mol addfile $file
> > }
> >
> >
> > ##
> > ## Make an atom selection, set the "User" fields for all atoms
> > ## in the selection ("all" in this case since I'm too lazy to do
> > ## something more interesting)
> > ##
> > set numframes [molinfo top get numframes]
> > set sel [atomselect top "all"]
> > for {set i 0} {$i<$numframes} {incr i} {
> > animate goto $i
> > $sel frame $i
> > puts "Setting User data for frame [$sel frame] ..."
> > $sel set user $i
> > }
> > $sel delete
> >
> > ##
> > ## change the "color by" and "trajectory" tab settings so that
> > ## the new color values, and start it animating...
> > ##
> > mol modcolor 0 0 User
> > mol colupdate 0 0 1
> > mol scaleminmax 0 0 0.0 $numframes
> > animate forward
> >
> >
> >
> >
> >
> > On Sun, Mar 21, 2004 at 04:05:23PM +0100, Cosmin ROMAN wrote:
> > > Hello,
> > >
> > > I would like to know how is the "User" coloring method supposed to work.
> I have been trying to read it from the user's guide but all it says there is
> simply "Provides a single data value for each atom for each timestep". Can I
> supply to vmd a procedure that computes the atom color at each time frame,
> or I should provide it a kind of a list.
> > >
> > > Thank you,
> > > Cosmin
> > >
> > > :*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:
> > > :
> > > Cosmin ROMAN, Ph.D. Student.
> > > :
> > > TIMA-INPG, MNS Group,
> > > : 46 Avenue Félix Viallet,
> > > 38031 Grenoble Cedex, FRANCE.
> > > :
> > > Tel : 00 33 4 76 57 48 34
> > > : Fax : 00 33 4 76 47 38 14
> > > e-mail : cosmin.roman_at_imag.fr
> > > :
> > > :*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:
> >
> > --
> > 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