VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Mar 18 2013 - 13:29:23 CDT

Hi Yohann,

I'm not sure what you are trying to do, but writing a script yourself is
probably the easiest way of doing what you want. The test.pdb you
included only had one frame in it, so you can get away with something
very simple:

set sel [atomselect top "beta > 0.5"]
$sel set radius 10

And be done! If you do need multiple frames that each have their own
beta values, you'll have to do something more complicated (as betas and
radii are not stored per frame, but are consistent for the same molecule).

-Josh Vermaas

On 03/18/2013 06:17 AM, Yohann Morille wrote:
> Hi !
>
> I have slightly modified the pdbbfactor.tcl script
> to read the b-factor within my pdb file and to change the radius of atoms
> with a b-factor greater than a threshold (0.5 in my example).
> To do that, I use atomselect within a loop but only the first atom is
> modified
> and I don't understand why.
>
> if anyone has an idea...
> thanks,
> Y.
>
>
>