Hi Doug,
scaling to the range of observed values:
stored.b = []
iterate n. CA, stored.b.append(b)
stored.min = min(stored.b)
stored.range = max(stored.b) - stored.min
alter n. CA, vdw = (b - stored.min) / stored.range * 4 + 1
rebuild
However, since the b-factor scales to the mean square displace
Hi Jason,
Thanks -- is there any way to add some limits to the scaling, say to alter the
vdw radius from a value of 1 to 5 based on a b-factor range of values?
Doug
On Jul 31, 2012, at 4:44 PM, Jason Vertrees wrote:
> Hi Douglas,
>
> You can do something as simple as this:
>
> # fetch a pr
Hi Douglas,
You can do something as simple as this:
# fetch a protein
fetch 1ejg, async=0
# show as spheres
as spheres, n. CA
# set the vdw radii = some factor of the b-factor
alter n. CA, vdw=b/5
rebuild
Cheers,
-- Jason
On Tue, Jul 31, 2012 at 3:36 PM, Douglas Kojetin
wrote:
> Hi All,
Hi All,
I would like to set the sphere size for each Ca atom proportional to the
b-factor value (the larger the b-factor the larger the sphere size) and also
color the sphere based on the b-factor value. Is there an easy way to adjust
the sphere size according to b-factor value?
Thanks,
Doug
