VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 14 2012 - 17:44:44 CDT

I'd have to know precisely what you did at the command line when
you started VMD, in order to determine the order of what file(s) you
have tried to load and what the atom selection commands actually got.
Did you try doing a "$sel num" to make sure that some atoms were actually
selected and assigned to the new type?

Cheers,
  John

On Fri, Sep 14, 2012 at 09:51:36PM +0000, Teich-McGoldrick, Stephanie wrote:
> Hello John,
>
> Thanks for the fast reply. Am I incorrect in thinking that I can assign
> atoms to 'Type B' after I have loaded the original molecule. I thought the
> line of code '$sel_B set type B' would define a new type called 'B', is
> this not correct? More specifically, the line of code I shared is within
> a user added key that I execute after load the molecule:
>
> user add key Control-f {
> set sel_B [atomselect top "charge = -0.820"]
> $sel_B set radius 0.5
> $sel_B set type B
> color Type B pink
>
> set molid [molinfo top]
> mol delrep 0 $molid
> mol representation VDW
> mol material "Bead"
> mol color Type
> mol addrep $molid
>
> }
>
>
> Thanks in advance,
> Stephanie
>
>
>
> On 9/14/12 3:46 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
>
> >Hi,
> > The color change command won't work if you don't have a structure
> >loaded with atoms matching "Type B" at the time the command is run.
> >I suspect you loaded something that didn't have a "Type B" in it.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Sep 14, 2012 at 09:40:04PM +0000, Teich-McGoldrick, Stephanie
> >wrote:
> >> Dear VMD users,
> >> I am using vmd 1.9.1, and receive the error message "ERROR) Unable to
> >> change color name" related to these lines in my .vmdrc file:
> >>
> >> set sel_B [atomselect top "charge = -0.820"]
> >>
> >> $sel_B set radius 0.5
> >>
> >> $sel_B set type B
> >>
> >> color Type B pink
> >>
> >> Specifically, the error is a result of the last line where I try to
> >>change
> >> the color of atom type B. Any advice would be greatly appreciated.
> >> Thanks in advance,
> >> Stephanie
> >
> >--
> >NIH Resource 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/ 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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078