VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 22 2007 - 13:44:19 CDT

Hi,
  Yes, you can change the default representation in a number of ways.
One of the easy ways is to set your preferred defaults using the
"mol default" commands, e.g.:
  mol default color {colorID 5}
  mol default style {NewCartoon 0.300000 6.000000 4.100000 0}
  mol default selection {name CA}
  mol default material {Transparent}

If you read Axel's CPMD-VMD tutorial, I believe he's also shown how
to accomplish similar things using other methods, which could be made
even more sophisticated if you want to do different reps depending on
what type of structure is loaded. Without going into the details since
it's preliminary, I plan to extend VMD to allow people to do this far more
easily in future versions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 22, 2007 at 12:37:41PM -0600, Jim Pfaendtner wrote:
> Dear VMD-L,
>
> What is the best way to automate my preferred graphic representation
> of a protein? For example, if I am working on a particular system
> with 100 residues and I always like 1-25 to be in "new cartoon / blue
> ", 26-50 to be in "new cartoon / red" , etc. How should I go about
> doing this? Can changes to the representation be made via a TCL script?
>
> thank you,
>
> Jim 

-- 
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