[Chimera-users] domains as ellipsoids?
Miguel Ortiz Lombardia
miguel.ortiz-lombardia at afmb.univ-mrs.fr
Thu Jul 30 00:35:10 PDT 2009
This is really great!
Thanks a lot for this feature!
Le 28 juil. 09 à 12:26, Stefano Ciurli a écrit :
> Thanks a lot Elaine, it works very well
> 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
>> 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 C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>> 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.
>>> 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
>>> or just click the Help button on the dialog to see your local copy
>>> this information. Eventually we want to also allow defining
>>> centroids and planes, but only the axes measurements are available
>>> Please send chimera questions to chimera-users at cgl.ucsf.edu rather
>>> than to me personally, unless private data are included. This
>>> others to benefit, or to answer the question if I am unavailable.
>>> I hope this helps,
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Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
163 Avenue de Luminy
13288 Marseille cedex 9
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
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