VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 28 2007 - 17:12:51 CDT

Bob,
  I've attached a patch that adds "user2", "user3", and "user4" fields
to the atom selection and graphical user interfaces. Feel free to
duplicate the logic to create as many user-defined fields as you like.
This patch is against the current VMD CVS, so that's probably what
you'll want to build against. If you or others have any trouble
compiling, let me know and I can provide you with a test build that
has these extra fields compiled in already. I've also attached a
toy script to exercise one of the new fields so you can easily
verify it is working for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 28, 2007 at 05:30:01PM -0400, Bob Johnson wrote:
> Hi John,
> Thanks for your response. For the analysis I'm trying to do, I think I really
> need extra user fields. If it's not too much trouble, could you provide some
> advice on how to alter the source code?
> Thanks,
> Bob
>
>
> Quoting John Stone <johns_at_ks.uiuc.edu>:
>
> >
> > Bob,
> > At present there is only a single per-timestep "user" field, but
> > it is actually pretty easy to create new user-defined fields. I have
> > been planning on making it possible to create and define new
> > per-timestep user-defined fields on-the-fly but haven't gotten around
> > to doing it yet. Creating and naming new fields is trivial, I just
> > have to come up with a clean way to add/delete dynamically created field
> > names into the atom selection language.
> >
> > If you like, I can tell you how to make a few of small changes to
> > the VMD source to add as many new per-timestep fields as you want.
> > You'd have to compile from source, but that's the easiest way to get
> > it done until I've implemented a more general solution.
> >
> > Cheers,
> > John Stone
> >
> > On Fri, Sep 28, 2007 at 05:15:05PM -0400, Bob Johnson wrote:
> > > Hello everyone,
> > > I would like to store the values of multiple time varying variables in the
> > user
> > > field. For example, I would like to store the RMSD values between each
> > frame
> > > and two (or maybe more) reference structures. Ideally, it would be great if
> > the
> > > user field per frame were an array that could store multiple values and be
> > > accessed via something like: $sel get user(i) Here i is the index of each
> > value
> > > stored in the array. Is there a way to do this?
> > > Thanks,
> > > Bob
> >
> > --
> > 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