Warren,
this thread gave me an idea about an enhancement request I had for some time.
Would it be possible to extend the molecular object module in a way that 2 or
more general properties per atoms would be available in PyMol in addition to b
and q. For instance in Grasp 2 properties (Prop1, Prop2) are available, which
can be used to visualize user defined properties, like distance of an atom from
other atoms, partial charges or any other computed property. Right now if one
wants to display these properties they have to be placed into either b and q,
which actually may contain values one likes to keep around.
This probably requires some serious reworking of the internals, but may be
worth the effort.
Cheers
Carsten
> -----Original Message-----
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of DeLano
> Scientific
> Sent: Friday, February 22, 2008 2:39 PM
> 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
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