VMD-L Mailing List

From: Aitor Gonzalez (agonzale_at_EMBL-Heidelberg.de)
Date: Mon Apr 09 2001 - 08:17:52 CDT

Hi Justin,

is there something similar to use with python? Which command is the
equivalent as 'trace' in python?

Let's say, that for me it's not so important to change the represantation
in each frame, but more the bonds between the atoms.

I want also to suggest you to improve the documentation refering to the
python commands. As you wrote some days ago, python is very nice to write
complex scripts , but it has no value if there isn't a good documentation
where you can find all commands (like for TCL).

Thanks in advance.

Aitor Gonzalez

Tef: +49-(0)6221-452012
Heidelberg, Germany

On Wed, 4 Apr 2001, Justin Gullingsrud wrote:

> Hi,
>
> Say you want the first rep of the top molecule to be updated whenever you
> change frames. As long as the atom selection doesn't take too long to
> calculate, you could type something like this from the command line:
>
> proc myproc { foo bar baz } {
> set seltext [lindex [molinfo top get "{selection 0}"] 0]
> mol modselect 0 top $seltext
> }
> trace variable vmd_frame w myproc
>
> Replace "top" with the id of the molecule you want and "selection 0" with
> "selection n" for rep n+1.
>
> For moderately sized systems this is usually sufficient; distance-based atom
> selections were reimplemented in December 1999 to use a grid-based, O(n)
> algorithm that is much more efficient than the O(n*n) code in earlier versions
> of VMD.
>
> Hope this helps,
>
> Justin
>
>
> On Sat, Mar 31, 2001 at 11:02:23AM -0600, John Stone wrote:
> >
> > Hi Brian,
> > If I understand your question correctly, there is presently no way
> > for VMD to save representations or selections for a particular frame or
> > frames in an animation. The representation is set for "all frames",
> > when you animate, it just gets applied to subsequent frames until it
> > is changed again. When VMD was designed this decision was surely a good
> > one, as the amount of memory available on machines of the time was such
> > that saving anything on a per-frame basis would have been troublesome.
> > Now that many desktop computers are coming with 256MB of memory or more,
> > it may be practical for VMD to implement per-frame features where
> > reps, selections, or other data might be associated uniquely with a frame
> > or frames of a trajectory animation. The main concern I'd have is that
> > if we did provide a mechanism for setting such things on a per-frame basis,
> > we'd have to do some work to make it usable for most people, ideally there'd
> > be some new user interface that'd let you scroll down a timeline of the
> > trajectory setting reps, selections, etc over certain spans of frames.
> >
> > I'd have to say though, that implementing all of that would probably be
> > something for "VMD 2.0" rather than an incremental evoluationary version.
> > We would probably want to redesign a lot of how VMD works in order to
> > accomodate stuff like that. VMD would need to become even more
> > "dynamics-centric" than it is presently.
> >
> > So, in answer to your question, I don't think there's any nice way to
> > do what you want. You could probably load in a bunch of frames as separate
> > molecules or something, but that has its own issues, and wouldn't let you
> > view the animation without using a script either.
> >
> > Thanks for using VMD,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Mar 30, 2001 at 11:40:43PM -0800, B. Bennion wrote:
> > > Hello,
> > > Does anyone know how to make a representation for a frame actually
> > > "stick"? When running through a set of frames using modselect, modstyle
> > > ... how can I make that frame keep that representation without having to
> > > rerun the scripts.
> > >
> > > For instance I am showing the hydration layer of a protein. The layer is
> > > calculated at each frame and then the representation altered through
> > > modselect. After the script is run, all the frames have the atom
> > > selections of the last frame and not their own time point.
> > >
> > > Any ideas
> > > Brian
> > >
> > > Graduate Research Assistant
> > > Dep. Medicinal Chemistry, University of Washington
> > > Tel# (206)616-2779
> > > BOX 357610 Seattle WA 98195
> > >
> > > email--bbennion_at_u.washington.edu
> > > web page--http://students.washington.edu/bbennion
> >
> > --
> > 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
>
> --
>
> Justin Gullingsrud 3111 Beckman Institute
> H: (217) 384-4220 I got a million ideas that I ain't even rocked yet...
> W: (217) 244-8946 -- Mike D
>