VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 27 2019 - 09:03:46 CST

Edward,
  Excellent. Yes, that's the main reason "logfile console" exists.
Glad that solved your problem.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 27, 2019 at 12:22:16PM +0100, Edward Ditler wrote:
> Hi,
>
> no, in fact I don???t actually need a list of all the parameters. What I was trying to do (and succeeded, thanks to Gianfranco), is to put all the changes in visualization I usually apply into my .vmdrc file.
>
> Instead of having an exhaustive list of commands, setting `logfile console` allows to see how the GUI is interacting with the scripting engine in the background. So that solved my problem.
>
>
> Best regards,
>
> Edward
>
> > Am 26.11.2019 um 17:33 schrieb John Stone <johns_at_ks.uiuc.edu>:
> >
> > Hi,
> > Do you really need all possible representations and their parameters,
> > or are you interested in a particular subset? Do you mind telling us what
> > you're trying to accomplish? Part of the reason the minutiae aren't listed
> > in the User's Guide is because we often change the underlying parameters
> > when new features are added.
> >
> > I would guess that a fully populated parameter list would add about
> > 20 pages to the User's guide since we'd have to explain the meaning of
> > many of the numerical parameters and their legal ranges (and then I'd have
> > to rewrite this text on every release since things always change here).
> >
> > If you can tell me more about what you're doing, I can help you get it done.
> >
> > Best regards,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Nov 26, 2019 at 09:23:58AM +0100, Edward Ditler wrote:
> >> Hello,
> >> I am trying to set the representation of my molecule programmatically. For
> >> many parts of the visualization, search engines manage to come up with the
> >> commands I'm looking for. Still I'm looking for a way to retrieve all
> >> possible arguments some of the functions take.
> >> If I try to set the bond resolution of my CPK rep, for example, the
> >> command will look something like
> >> ```
> >> vmd > mol modstyle 0 0 BondResolution 100
> >> ERROR) Unknown atom representation command 'BondResolution 100`.
> >> ```
> >> Now is there some command like `mol modstyle list` to get a list of all
> >> acceptable commands? The documentation
> >> at [1]http://www.ks.uiuc.edu/Research/vmd/current/ug/node140.html
> >> unfortunately doesn't say more than
> >> o modstyle rep_number molecule_number rep_style: Change the current
> >> rendering method (style) for the given representation in the specified
> >> molecule.
> >>
> >> and doesn't state which values rep_style can take.
> >> Thanks for your help!
> >> Best regards,
> >> Edward Ditler
> >> ---
> >> University of Zurich
> >> Edward Ditler
> >> Department of Chemistry B
> >> Research Group Luber
> >> Winterthurerstrasse 190
> >> CH-8057 Zurich
> >>
> >> Office: Y34-F92
> >> Phone: +41 44 635 46 43
> >> [2]E-Mail: edward.ditler_at_chem.uzh.ch
> >>
> >> References
> >>
> >> Visible links
> >> 1. http://www.ks.uiuc.edu/Research/vmd/current/ug/node140.html
> >> 2. mailto:edward.ditler_at_chem.uzh.ch
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
> >
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/