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...... > > > > 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 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.
