Resending with a smaller attachment.... -Tom
-----Original Message----- From: Thomas Stout Sent: Friday, February 22, 2008 9:57 AM To: 'Tsjerk Wassenaar' Cc: PyMOL-users@lists.sourceforge.net Subject: RE: [Junk released by Allow List] Re: [PyMOL] Isotropic thermal ellipsoids Yes!....essentially....I've just used it as: PyMOL>show spheres, ligand PyMOL>show sticks, ligand PyMOL>alter obj01, vdw=vdw*(b/100) PyMOL>rebuild and gotten more-or-less what I was looking for, but I would caution that a good "scaling" of the atom spheres based on B-factors requires both a more thoughtful approach and also some fine tuning if you want to accentuate differences when the range is small.... Thanks! -Tom PS - I've attached an example from PDB ID 1Z5M, but the attachment may very well get stripped... -----Original Message----- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Friday, February 22, 2008 1:11 AM To: Thomas Stout Cc: PyMOL-users@lists.sourceforge.net Subject: [Junk released by Allow List] 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 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.
<<attachment: iso-Bs_trim.jpg>>
