[Chimera-users] domains as ellipsoids?
stefano.ciurli at unibo.it
Tue Jul 28 03:26:01 PDT 2009
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 of
>> 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 allows
>> others to benefit, or to answer the question if I am unavailable.
>> I hope this helps,
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