From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 01 2016 - 15:40:57 CST

Any atom that has no value defaults to 0.0...

Cheers,
  John

On Thu, Dec 01, 2016 at 03:24:45PM -0600, Brian Radak wrote:
> 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: [1]radak_at_uchicago.edu
>
> References
>
> Visible links
> 1. mailto:radak_at_uchicago.edu

-- 
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