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...... > > > > This email (including any attachments) may contain material that is > > confidential and privileged and is for the sole use of the intended > > recipient. Any review, reliance or distribution by others or > > forwarding without express permission is strictly > prohibited. If you > > are not the intended recipient, please contact the sender > and delete > > all copies. > > > > > > Exelixis, Inc. reserves the right, to the extent and under > > circumstances permitted by applicable law, to retain, monitor and > > intercept e-mail messages to and from its systems. > > > > > > > > > ---------------------------------------------------------------------- > > --- This SF.net email is sponsored by: Microsoft Defy all > > challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > -- > 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 > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft Defy all > challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
