VMD-L Mailing List

From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Thu Dec 01 2016 - 15:24:45 CST

Aha! That will work just fine.

One last question. If I want to have a single representation with a
selection like:

protein and user

That just turns off the assigned atoms at each frame, what will happen
to the atoms that I /didn't/ flag (i.e. should always be present)? Is
there default value 0.0 if I didn't touch it? In that case I would
probably want to reverse my boolean assignments.

On 12/01/2016 03:11 PM, Vermaas, Joshua wrote:
> Hi Brian,
>
> A selection has a frame assigned to it, and you can't set it all at once
> from my experience (although that would be nice!). Instead, you loop
> over each frame, and assign the user field on a frame by frame basis.
>
> for { set f 0 } { $f < [molinfo top get numframes } { incr f } {
> $sel frame $f
> $sel set user [lindex $somegiant2Dlist $f]
> }
>
> This means that your property list needs to be 2-dimensional, and you
> need to iterate over every frame.
>
> -Josh
>
> On 12/01/2016 01:58 PM, Brian Radak wrote:
>> Apologies if this is a repeat.
>>
>> I am trying to make use of the "user" field in having a dynamic
>> representation that changes at each time step. This is just a simple
>> boolean that turns off or on a small set of atoms as part of a larger
>> selection.
>>
>> How does one assign a time series to the user field? For each atom I
>> have a Tcl list with size equal to the number of DCD frames, but the
>> following does not seem to work:
>>
>> % set myProperty <list of size equal to numframes>
>> % set sel [atomselect <selection for a single atom>]
>> % $sel set user $myProperty
>>
>> Is "user" not a time dependent property by default? The help message for
>> "atomselection set" does not seem to indicate any further keywords to
>> flag that.
>>
>> Brian
>> 

-- 
Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
email: radak_at_uchicago.edu