[Chimera-users] Ellipsoid using chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 20 09:04:41 PDT 2014


For both methods, it is important to only include the atoms you really want to include.  For example, you would not want to specify  an entire model or chain if it includes stuff like waters and ligands.  You could specify just the part you want as a residue number range, or as protein-only.  Consider also whether you want to include sidechain atoms or just the backbone.

Elaine

On Oct 20, 2014, at 8:56 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Anu,
> The "measure inertia" command reports the axes in the Reply Log (menu: Favorites… Reply Log).   So it would be possible to manually calculate angles from those values.  
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia>
> 
> However, in my opinion, it would be easier to use "define axis"  or  "define plane" on each of the domains (or the corresponding GUI, menu: Tools… Structure Analysis… Axes/Planes/Centroids).  That would create best-fit axis or plane objects on which you can easily perform measurements of distances and angles using either the Axes/Planes/Centroids GUI or the "distance" and "angle" commands.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
> 
> Differences:
> - Axes/Planes/Centroids doesn't make ellipsoids, it just calculates a best-fit axis or a best-fit plane… but you could still use the "measure inertia" ellipsoids for display
> 
> - "measure inertia" always uses mass-weighting for atoms, whereas Axes/Planes/Centroids doesn't mass-weight by default, but there are command and GUI options to turn it on
> 
> - if you use the same atoms and same parameters (e.g. mass-weighting), I believe the directions of the Axes/Planes/Centroids axis and the ellipsoid longest axis would be the same, and thus angles calculated from the two methods should be in agreement.  The lengths could be different because they are determined in different ways.  It is a similar situation for the ellipsoid two longest axes and the Axes/Planes/Centroids plane.
> 
> - Axes/Planes/Centroids  works only on atoms, not input surfaces, whereas "measure inertia" could work if you only had some surface without atoms… but this doesn't sound relevant to your situation anyway
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Oct 19, 2014, at 9:31 PM, Anu Chandran <miscofanu at gmail.com> wrote:
> 
>> Dear users,
>> I have used chimera to draw ellipsoid to represent each domain in a protein structure using the measure inertia command in an attempt to visualize the orientation of one domain with respect to the other. This has been done for a set of homologous structures of the same protein.
>> 
>> Now I want to visualize the axes of the ellipsoid of the two domains. Can anybody please suggest me on how to do it ?
>> 
>> Also Is there any way to quantitate the angle between the two ellipsoid representing the two domains in a protein ?
>> 
>> Thanking you,
>> 
>> with regards,
>> Anu
> 
> 
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