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Re: [PyMOL] Isotropic thermal ellipsoids
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From: DeLano S. <de...@de...> - 2008-02-27 01:09:38
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Carsten, Thank you for the suggestion. It has got me thinking... In the meantime, you can already use Python itself to store additional molecular properties which can be mapped to b, q, or vdw as needed using the "alter" command over various selection. However, I'm not sure that would enable exactly what you're thinking about doing, so perhaps you could describe one or more of your intended use cases in a little more detail? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf > Of Schubert, Carsten [PRDUS] > Sent: Sunday, February 24, 2008 11:12 AM > To: DeLano Scientific > Cc: PyM...@li... > Subject: Re: [PyMOL] Isotropic thermal ellipsoids > > 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: pym...@li... > > [mailto:pym...@li...]On Behalf > Of DeLano > > Scientific > > Sent: Friday, February 22, 2008 2:39 PM > > To: 'Tsjerk Wassenaar'; 'Thomas Stout' > > Cc: PyM...@li... > > 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:de...@de... > > > > > > > -----Original Message----- > > > From: pym...@li... > > > [mailto:pym...@li...] On Behalf Of > > > Tsjerk Wassenaar > > > Sent: Friday, February 22, 2008 1:11 AM > > > To: Thomas Stout > > > Cc: PyM...@li... > > > 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 > <ts...@ex...> > > > 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 > > > > PyM...@li... > > > > 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 > > > PyM...@li... > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > -------------------------------------------------------------- > > ----------- > > 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 > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > -------------------------------------------------------------- > ----------- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |