[Chimera-users] domains as ellipsoids?

Stefano Ciurli 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  
> 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 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,
>> Elaine

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