[Chimera-users] domains as ellipsoids?

Thomas Goddard goddard at cgl.ucsf.edu
Thu Jul 30 11:01:45 PDT 2009

Hi Miguel,

   Here's an example of inertia ellipsoids for chains of photosystem II.



-------- Original Message --------
Subject: Re: [Chimera-users] domains as ellipsoids?
From: Miguel Ortiz Lombardia
To: Chimera BB <chimera-users at 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 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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