VMD-L Mailing List

From: Teich-McGoldrick, Stephanie (steichm_at_sandia.gov)
Date: Fri Sep 14 2012 - 20:01:04 CDT

Hello John,

Thanks for the suggestion. Testing this led me to realize, that although
my charge is -0.820 in my data file, vmd lists the charge as -0.8199999.
My code works if I change my script to read:

set sel_B [atomselect top "charge > -0.83 and charge < -0.81"]

Thanks again,
Stephanie

On 9/14/12 4:44 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:

>
>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
>