VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 26 2006 - 14:03:29 CST

Hi guys,
  There's also a new "mol default" command that you can use for
this purpose in the test versions of VMD 1.8.4. Here's an example
of how you'd use it in your .vmdrc file:
  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}

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 25, 2006 at 07:53:15AM -0500, Axel Kohlmeyer wrote:
>
> On Wed, 25 Jan 2006, Adrian Koh wrote:
>
> AK> Hi,
>
> adrian,
>
> AK>
> AK> How could I change the default graphical representations in vmd.rc
> AK> file? What is the script to change the default "Coloring Method" and
> AK> "Drawing Method" under the "Draw Style" menu?
>
> due to some technical reasons, this is currently not directly possible,
> see the following URL for a workaround.
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect2
>
> AK> I found in the manual, pg. 105, that a probable command would be "mol
> AK> color /coloring_method/", I've filled in "Element" for the
> AK> "coloring_method" but nothing happened. How do we know what to fill in
> AK> place of the italicized commands shown in the manual?
>
> it is not that simple. this command will set the default for the
> next new representation, but the first representation is hardcoded
> into VMD. to change the color of an existing representation, you
> need to use 'mol modcolor...' and 'mol modstyle ...' and so on.
>
> i suggest you create a visualization and then save the state and look
> at the generated file. search for 'mol new' and this is where the
> loading of a molecule and creation of a representation happens on
> the script level. you will see, that it first deletes the default.
>
> another way to deal with that issue (because there are potential
> performance problems on huge molecules with other reps than lines)
> is to have a minimal 'template' script file to load a molecule in
> the style you want it (e.g. created from a saved state file by deleting
> everything unwanted) and then just change the filename and load that
> state/script file instead of the molecule.
>
> regards,
> axel.
>
> AK>
> AK> Thanks!
> AK>
> AK> Regards,
> AK> Adrian.
> AK>
> AK>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
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