## Re: [PyMOL] Isotropic thermal ellipsoids

 Re: [PyMOL] Isotropic thermal ellipsoids From: DeLano Scientific - 2008-02-22 19:39:17 ```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:delsci@... > -----Original Message----- > From: pymol-users-bounces@... > [mailto:pymol-users-bounces@...] On Behalf > Of Tsjerk Wassenaar > Sent: Friday, February 22, 2008 1:11 AM > To: Thomas Stout > Cc: PyMOL-users@... > 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 > 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@... > > 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@... > https://lists.sourceforge.net/lists/listinfo/pymol-users ```

 [PyMOL] Isotropic thermal ellipsoids From: Thomas Stout - 2008-02-22 00:49:48 Attachments: Message as HTML ```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. ```
 Re: [PyMOL] Isotropic thermal ellipsoids From: Tsjerk Wassenaar - 2008-02-22 09:11:22 ```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 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@... > 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 ```
 Re: [PyMOL] Isotropic thermal ellipsoids From: DeLano Scientific - 2008-02-22 19:39:17 ```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:delsci@... > -----Original Message----- > From: pymol-users-bounces@... > [mailto:pymol-users-bounces@...] On Behalf > Of Tsjerk Wassenaar > Sent: Friday, February 22, 2008 1:11 AM > To: Thomas Stout > Cc: PyMOL-users@... > 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 > 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@... > > 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@... > https://lists.sourceforge.net/lists/listinfo/pymol-users ```
 Re: [PyMOL] Isotropic thermal ellipsoids From: Thomas Stout - 2008-02-22 19:49:34 ```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:delsci@...] Sent: Friday, February 22, 2008 11:39 AM To: 'Tsjerk Wassenaar'; Thomas Stout Cc: PyMOL-users@... 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:delsci@... > -----Original Message----- > From: pymol-users-bounces@... > [mailto:pymol-users-bounces@...] On Behalf > Of Tsjerk Wassenaar > Sent: Friday, February 22, 2008 1:11 AM > To: Thomas Stout > Cc: PyMOL-users@... > 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 > 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@... > > 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@... > 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. ```
 Re: [PyMOL] Isotropic thermal ellipsoids From: Tsjerk Wassenaar - 2008-02-22 20:43:10 ```Hi, My solution was mainly aimed at offering a general method for using some property (presumably available in the b-factor field) to be reflected in the size of the spheres, as I recall was asked for. But the math to go from b-factor in the b-factor field to 'isotropic thermal motion approximation' should of course be performed as given by Warren. I sometimes use it for displaying RMSF vaues from a simulation. Actually, for the interested, the math library ('from math import *') offers many other operations to aid in such displaying. Applying a log-transformation may for example be useful to visualize properties which range over several orders of magnitude (non-linearly). Cheers, Tsjerk On Fri, Feb 22, 2008 at 8:49 PM, Thomas Stout wrote: > > 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:delsci@...] > Sent: Friday, February 22, 2008 11:39 AM > To: 'Tsjerk Wassenaar'; Thomas Stout > Cc: PyMOL-users@... > > > 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:delsci@... > > > > -----Original Message----- > > From: pymol-users-bounces@... > > [mailto:pymol-users-bounces@...] On Behalf > > Of Tsjerk Wassenaar > > Sent: Friday, February 22, 2008 1:11 AM > > To: Thomas Stout > > Cc: PyMOL-users@... > > 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 > > 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@... > > > 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@... > > 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. > > -- 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 ```
 Re: [PyMOL] Isotropic thermal ellipsoids From: Schubert, Carsten [PRDUS] - 2008-02-24 19:11:48 ```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-bounces@... > [mailto:pymol-users-bounces@...]On Behalf Of DeLano > Scientific > Sent: Friday, February 22, 2008 2:39 PM > To: 'Tsjerk Wassenaar'; 'Thomas Stout' > Cc: PyMOL-users@... > 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:delsci@... > > > > -----Original Message----- > > From: pymol-users-bounces@... > > [mailto:pymol-users-bounces@...] On Behalf > > Of Tsjerk Wassenaar > > Sent: Friday, February 22, 2008 1:11 AM > > To: Thomas Stout > > Cc: PyMOL-users@... > > 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 > > 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@... > > > 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@... > > 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 > PyMOL-users@... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > ```
 Re: [PyMOL] Isotropic thermal ellipsoids From: DeLano Scientific - 2008-02-27 01:09:38 ```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:delsci@... > -----Original Message----- > From: pymol-users-bounces@... > [mailto:pymol-users-bounces@...] On Behalf > Of Schubert, Carsten [PRDUS] > Sent: Sunday, February 24, 2008 11:12 AM > To: DeLano Scientific > Cc: PyMOL-users@... > 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: pymol-users-bounces@... > > [mailto:pymol-users-bounces@...]On Behalf > Of DeLano > > Scientific > > Sent: Friday, February 22, 2008 2:39 PM > > To: 'Tsjerk Wassenaar'; 'Thomas Stout' > > Cc: PyMOL-users@... > > 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:delsci@... > > > > > > > -----Original Message----- > > > From: pymol-users-bounces@... > > > [mailto:pymol-users-bounces@...] On Behalf Of > > > Tsjerk Wassenaar > > > Sent: Friday, February 22, 2008 1:11 AM > > > To: Thomas Stout > > > Cc: PyMOL-users@... > > > 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 > > > > 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@... > > > > 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@... > > > 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 > > PyMOL-users@... > > 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 > PyMOL-users@... > https://lists.sourceforge.net/lists/listinfo/pymol-users ```