Re: [Chimera-users] domains as ellipsoids?
On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote:
Hello Elaine, I am writing to ask you the following: I need to define the relative orientation of two domains of a protein, and I am not sure about how to do it. I was thinking of approximating the domains as ellipsoids and then calculate the angles between the axes of the ellipsoids. I wonder if you have a better way to define the orientation, or if Chimera can do things like calculate ellipsoids axes and their orientation. Regards Stefano
Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes> or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently. Please send chimera questions to chimera-users@cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Thank you Elaine, I will try to follow the advice and instructions Stefano On 24 lug 2009, at 18:57, Elaine Meng wrote:
On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote:
Hello Elaine, I am writing to ask you the following: I need to define the relative orientation of two domains of a protein, and I am not sure about how to do it. I was thinking of approximating the domains as ellipsoids and then calculate the angles between the axes of the ellipsoids. I wonder if you have a better way to define the orientation, or if Chimera can do things like calculate ellipsoids axes and their orientation. Regards Stefano
Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes>
or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently.
Please send chimera questions to chimera-users@cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Hi Stefano, This may not help with your specific problem, but there is a new command to create ellipsoids for specified sets of atoms. To use it you need a daily build dated July 26, 2009 or later. It is not documented yet, but here is usage and some information: Usage: measure inertia atom-spec [perChain true|false] [color colorname] Examples: measure inertia :1-11.a measure inertia #0 perChain true measure inertia ligand color green "measure" and "inertia" are literal, atom-spec is a command-line atom specifier, the perChain option means to calculate an ellipsoid for every chain in the specified set of atoms. The ellipsoid(s) will be shown in the graphics window as a surface model, and information (described below) about the ellipsoid will be sent to the Reply Log. This command does not tell you the relationships between different ellipsoids, only information about each ellipsoid individually. However, you can use standard vector arithmetic procedures on the information in the Reply Log to get angles between the vectors or planes of different ellipsoids. The measure inertia command is mass weighted. There is no option to weight atoms equally. Here are more details about the output. The vectors v1, v2, and v3 are the principle axes (longest to shortest). The axis lengths are called a, b, c (half diameter of ellipsoid along axes v1, v2 and v3). And the moments are given as sqrt(inertia/mass) about each axis, called r1, r2 and r3. The meaning of r1 is that it is the radius away from axis v1 where you could put all the mass to have the same moment of inertia about v1 as the molecule. So r1, r2, and r3 are effective radii about the axes v1, v2, v3. There is a perChain option that makes a separate ellipsoid for each chain using the specified atoms. If no color is specified it matches the first atom's color. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote:
Hello Elaine, I am writing to ask you the following: I need to define the relative orientation of two domains of a protein, and I am not sure about how to do it. I was thinking of approximating the domains as ellipsoids and then calculate the angles between the axes of the ellipsoids. I wonder if you have a better way to define the orientation, or if Chimera can do things like calculate ellipsoids axes and their orientation. Regards Stefano
Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes>
or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently.
Please send chimera questions to chimera-users@cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable.
I hope this helps, Elaine
Thanks a lot Elaine, it works very well Stefano On 28 lug 2009, at 0:17, Elaine Meng wrote:
Hi Stefano, This may not help with your specific problem, but there is a new command to create ellipsoids for specified sets of atoms. To use it you need a daily build dated July 26, 2009 or later.
It is not documented yet, but here is usage and some information:
Usage: measure inertia atom-spec [perChain true|false] [color colorname]
Examples: measure inertia :1-11.a measure inertia #0 perChain true measure inertia ligand color green
"measure" and "inertia" are literal, atom-spec is a command-line atom specifier, the perChain option means to calculate an ellipsoid for every chain in the specified set of atoms. The ellipsoid(s) will be shown in the graphics window as a surface model, and information (described below) about the ellipsoid will be sent to the Reply Log. This command does not tell you the relationships between different ellipsoids, only information about each ellipsoid individually. However, you can use standard vector arithmetic procedures on the information in the Reply Log to get angles between the vectors or planes of different ellipsoids.
The measure inertia command is mass weighted. There is no option to weight atoms equally. Here are more details about the output. The vectors v1, v2, and v3 are the principle axes (longest to shortest). The axis lengths are called a, b, c (half diameter of ellipsoid along axes v1, v2 and v3). And the moments are given as sqrt(inertia/mass) about each axis, called r1, r2 and r3. The meaning of r1 is that it is the radius away from axis v1 where you could put all the mass to have the same moment of inertia about v1 as the molecule. So r1, r2, and r3 are effective radii about the axes v1, v2, v3.
There is a perChain option that makes a separate ellipsoid for each chain using the specified atoms. If no color is specified it matches the first atom's color.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote:
Hello Elaine, I am writing to ask you the following: I need to define the relative orientation of two domains of a protein, and I am not sure about how to do it. I was thinking of approximating the domains as ellipsoids and then calculate the angles between the axes of the ellipsoids. I wonder if you have a better way to define the orientation, or if Chimera can do things like calculate ellipsoids axes and their orientation. Regards Stefano
Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes>
or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently.
Please send chimera questions to chimera-users@cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable.
I hope this helps, Elaine
This is really great! Thanks a lot for this feature! Miguel Le 28 juil. 09 à 12:26, Stefano Ciurli a écrit :
Thanks a lot Elaine, it works very well Stefano
On 28 lug 2009, at 0:17, Elaine Meng wrote:
Hi Stefano, This may not help with your specific problem, but there is a new command to create ellipsoids for specified sets of atoms. To use it you need a daily build dated July 26, 2009 or later.
It is not documented yet, but here is usage and some information:
Usage: measure inertia atom-spec [perChain true|false] [color colorname]
Examples: measure inertia :1-11.a measure inertia #0 perChain true measure inertia ligand color green
"measure" and "inertia" are literal, atom-spec is a command-line atom specifier, the perChain option means to calculate an ellipsoid for every chain in the specified set of atoms. The ellipsoid(s) will be shown in the graphics window as a surface model, and information (described below) about the ellipsoid will be sent to the Reply Log. This command does not tell you the relationships between different ellipsoids, only information about each ellipsoid individually. However, you can use standard vector arithmetic procedures on the information in the Reply Log to get angles between the vectors or planes of different ellipsoids.
The measure inertia command is mass weighted. There is no option to weight atoms equally. Here are more details about the output. The vectors v1, v2, and v3 are the principle axes (longest to shortest). The axis lengths are called a, b, c (half diameter of ellipsoid along axes v1, v2 and v3). And the moments are given as sqrt(inertia/mass) about each axis, called r1, r2 and r3. The meaning of r1 is that it is the radius away from axis v1 where you could put all the mass to have the same moment of inertia about v1 as the molecule. So r1, r2, and r3 are effective radii about the axes v1, v2, v3.
There is a perChain option that makes a separate ellipsoid for each chain using the specified atoms. If no color is specified it matches the first atom's color.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote:
Hello Elaine, I am writing to ask you the following: I need to define the relative orientation of two domains of a protein, and I am not sure about how to do it. I was thinking of approximating the domains as ellipsoids and then calculate the angles between the axes of the ellipsoids. I wonder if you have a better way to define the orientation, or if Chimera can do things like calculate ellipsoids axes and their orientation. Regards Stefano
Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes>
or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently.
Please send chimera questions to chimera-users@cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable.
I hope this helps, Elaine
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-- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2
Hi Miguel, Here's an example of inertia ellipsoids for chains of photosystem II. http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/photosystemII/psii.html Tom -------- Original Message -------- Subject: Re: [Chimera-users] domains as ellipsoids? From: Miguel Ortiz Lombardia To: Chimera BB <chimera-users@cgl.ucsf.edu> Date: 7/30/09 12:35 AM
This is really great! Thanks a lot for this feature!
Miguel
Le 28 juil. 09 à 12:26, Stefano Ciurli a écrit :
Thanks a lot Elaine, it works very well Stefano
On 28 lug 2009, at 0:17, Elaine Meng wrote:
Hi Stefano, This may not help with your specific problem, but there is a new command to create ellipsoids for specified sets of atoms. To use it you need a daily build dated July 26, 2009 or later.
It is not documented yet, but here is usage and some information:
Usage: measure inertia atom-spec [perChain true|false] [color colorname]
Examples: measure inertia :1-11.a measure inertia #0 perChain true measure inertia ligand color green
"measure" and "inertia" are literal, atom-spec is a command-line atom specifier, the perChain option means to calculate an ellipsoid for every chain in the specified set of atoms. The ellipsoid(s) will be shown in the graphics window as a surface model, and information (described below) about the ellipsoid will be sent to the Reply Log. This command does not tell you the relationships between different ellipsoids, only information about each ellipsoid individually. However, you can use standard vector arithmetic procedures on the information in the Reply Log to get angles between the vectors or planes of different ellipsoids.
The measure inertia command is mass weighted. There is no option to weight atoms equally. Here are more details about the output. The vectors v1, v2, and v3 are the principle axes (longest to shortest). The axis lengths are called a, b, c (half diameter of ellipsoid along axes v1, v2 and v3). And the moments are given as sqrt(inertia/mass) about each axis, called r1, r2 and r3. The meaning of r1 is that it is the radius away from axis v1 where you could put all the mass to have the same moment of inertia about v1 as the molecule. So r1, r2, and r3 are effective radii about the axes v1, v2, v3.
There is a perChain option that makes a separate ellipsoid for each chain using the specified atoms. If no color is specified it matches the first atom's color.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote:
Hello Elaine, I am writing to ask you the following: I need to define the relative orientation of two domains of a protein, and I am not sure about how to do it. I was thinking of approximating the domains as ellipsoids and then calculate the angles between the axes of the ellipsoids. I wonder if you have a better way to define the orientation, or if Chimera can do things like calculate ellipsoids axes and their orientation. Regards Stefano
Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes>
or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently.
Please send chimera questions to chimera-users@cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable.
I hope this helps, Elaine
participants (4)
-
Elaine Meng -
Miguel Ortiz Lombardia -
Stefano Ciurli -
Thomas Goddard