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
Dear PyMol users!
I have pdb structure wich I'd like to prepare for my MD simulation. In
that case this structure consist of some non-standart residue (
chromophore) wich is covalently bonded to the protein's backbone. The
main problem is that this structure has some missing residues on both
of t
Hi Anke,
> we are currently trying to do movies and are running into some problems
> concerning the “auto interpolate” function of pymol. We realized that camera
> and molecule positions are always interpolated back to the position of frame
> 1 at the end of the movie.
Autointerpolate is not the
Hi Pascal,
the problem is that PyMOL looks up atoms by "ID", which are not unique
in your structure. Possible workarounds:
1) disable dynamic measures:
PyMOL> unset dynamic_measures
2) assign unique atom IDs:
PyMOL> stored.ID = 0
PyMOL> alter all, ID=stored.ID=stored.ID+1
Cheers,
Thomas
Pa
