Hi,
My solution was mainly aimed at offering a general method for using
some property (presumably available in the b-factor field) to be
reflected in the size of the spheres, as I recall was asked for. But
the math to go from b-factor in the b-factor field to 'isotropic
thermal motion approximation' should of course be performed as given
by Warren. I sometimes use it for displaying RMSF vaues from a
simulation.
Actually, for the interested, the math library ('from math import *')
offers many other operations to aid in such displaying. Applying a
log-transformation may for example be useful to visualize properties
which range over several orders of magnitude (non-linearly).
Cheers,
Tsjerk
On Fri, Feb 22, 2008 at 8:49 PM, Thomas Stout <tst...@exelixis.com> wrote:
>
> Warren is absolutely correct & I hope I prefaced my original question
> sufficiently to indicate that this is an entirely "silly" thing to do &
> would likely cause more confusion than it's worth, but I wanted to
> illustrate a specific, _qualitative_ point to a colleague and so wanted
> to construct such an image.... On top of all the other valid points
> Warren made, one should also keep in mind that at anything less than
> ultra-high (atomic) resolution (0.8-1.0A resolution), constraints are
> applied by refinement protocols. Thermal parameters are generally
> restrained by a Gaussian to limit their deviation from the values
> attained by atoms to which covalent bonds are formed, operating under
> the assumption that such linked atoms will move in some sort of
> harmonic. Thus, B-factors (within a molecule) can be compared as trends
> along a set of linked atoms, but individual values can only be assessed
> in regard to the values of the atoms around them....etc etc etc... The
> caveats go on......
>
> I don't recommend it for general use or analysis!!
> -Tom
>
>
> -----Original Message-----
> From: DeLano Scientific [mailto:del...@delsci.info]
> Sent: Friday, February 22, 2008 11:39 AM
> To: 'Tsjerk Wassenaar'; Thomas Stout
> Cc: PyMOL-users@lists.sourceforge.net
>
>
> Subject: RE: [PyMOL] Isotropic thermal ellipsoids
>
> Tsjerk,
>
> Close, but the relationship isn't linear. RMS displacement is
> c*sqrt(temperature-factor), where c is a constant. The following
> equation
> can be found in crystallography texts:
>
> B = U * 8 * pi^2.
>
> where U is a mean squared displacement and B is the temperature factor.
> If
> I've done the math correctly, then the PyMOL input to show
> root-mean-squared
> (RMS) displacement would be:
>
> from math import sqrt,pi
> alter all, vdw = sqrt(b/8)/pi
> show spheres
>
> However, given all the fitting performed in the data reduction and
> structure
> refinement, absolute temperature factors many not be a reliable measure
> of
> absolute RMS displacement in any sort of modeling or analysis work.
>
> It is probably safer to stick with relative, qualitative comparisons
> within
> a single structure, keeping in mind that vdw could be scaled by
> systematic
> biases.
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:del...@delsci.info
>
>
> > -----Original Message-----
> > From: pymol-users-boun...@lists.sourceforge.net
> > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> > Of Tsjerk Wassenaar
> > Sent: Friday, February 22, 2008 1:11 AM
> > To: Thomas Stout
> > Cc: PyMOL-users@lists.sourceforge.net
> > Subject: Re: [PyMOL] Isotropic thermal ellipsoids
> >
> > Hi Tom,
> >
> > Does what you're trying to do come down to:
> >
> > alter all, vdw=b/100
> > show spheres
> >
> > ?
> >
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Fri, Feb 22, 2008 at 1:42 AM, Thomas Stout
> > <tst...@exelixis.com> wrote:
> > >
> > >
> > > Hi All --
> > >
> > > Yes, I know I want to do something silly here, but does
> > anyone know of
> > > a "jiffy" that will generate anisotropic thermal parameters for an
> > > isotropic atom?
> > >
> > > My end goal is to create a figure showing a ligand as
> > ball-and-stick
> > > where the spheres are scaled by the B-factor. Since I'm
> > not dealing
> > > with ultra-high resolution data, I just have normal
> > isotropic atoms.
> > > I'd like to use the new "ellipsoids" functionality in PyMOL, but it
> > > requires anisotropic atom lines. Obviously, I could write a python
> > > script that would scale the vdW radii by some normalization of the
> > > B-factor, but I thought I could be lazy and use what Warren
> > has already built into PyMOL.....
> > >
> > > Thanks!
> > > -Tom
> > >
> > > PS -- I'm thinking of something like the "-iso" feature of
> > rastep in
> > > Ethan Merritt's Raster3D suite......
> > >
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
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> prohibited. If you are not the intended recipient, please
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>
>
> Exelixis, Inc. reserves the right, to the extent and under
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
