[chimerax-users] Identifying symmetry of a model

[Elaine Meng]

You probably already knew this, but the RCSB PDB reports symmetry and pseudosymmetry.  E.g. 4hhb (alpha2 beta2 hemoglobin) is C2 symmetric and D2 pseudosymmetric.  I also like the quaternary-structure diagrams shown in the 3D Complex database: <http://www.3dcomplex.org/>

ChimeraX also shows subunit diagrams, and sometimes these help in understanding symmetry and/or pseudosymmetry of large complexes.   For example,

open 3cx5
interfaces protein

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>

... it may take a while because it's based on calculated buried surface areas.  A screenshot of the resulting interactive diagram  is attached.

Best,
Elaine



> On Jan 18, 2021, at 10:09 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Yaikhomba,
> ChimeraX doesn't have anything to automatically identify the symmetry of an atomic structure.  There is only "measure symmetry" for maps, which is also somewhat limited in assuming standard orientations, etc.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry>
> 
> However, say you have identified the approximate symmetry by eye.  One possibility for C2 symetry is to open two copies of the structure, and then superimpose so that one half in one copy is on top of the other half of the other copy, then measure the rotation between the two.  However, if the symmetry is only approximate, it is your own judgment call of which atoms are best to match to which atoms to obtain the best superposition of the halves.
> 
> Example:
> open 3cx5
> open 3cx5
> mm #1/D to #2/O 
> measure rotation #1 to #2
> 
> ... the measurement shows an axis which is really two markers (fake atoms) connected by a link (bond).  You can manually orient the view to put that axis along the line of sight. You may need to temporarily hide the atomic models (e.g. with checkboxes in the Models panel) to see it clearly.  Then you can hide the axis model if you want and turn the atomic models display back on.
> 
> Chimera had an "align" command to put two atoms or markers along the line of sight, but ChimeraX does not have that feature.  (ChimeraX "align" does something different, it superimposes atoms.  You could use it to do the superposition, or use "mm" aka "matchmaker" as in my example above)
> 
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
> 
> For your 4 residues case, you could define a plane from those residues (displayed as a flat disc) with "define" and then (again manually) rotate the view so that the plane is perpendicular to the line of sight.  You can hide atomic models and/or hide the plane at any step with the Model panel checkboxes, as above.
> 
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#plane>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jan 18, 2021, at 9:02 AM, Y. Mutum <ym337 at cam.ac.uk> wrote:
>> 
>> Hi 
>> 
>> I am working with pdb id: 3cx5. This model is roughly C2 symmetric.
>> Is there a way to identify the symmetry (or rough symmetry of a not-so symmetric model) of a pdb/ mmcif model and orient the symmetry axis to the axis perpendicular to the screen?
>> 
>> On a similar note, say we select a 4 somewhat symmetry-related residues in this model and make 2 intersecting lines, is there a way to align these lines perpendicular to the perpendicular screen axis?
>> 
>> Thanks
>> Yaikhomba
> 
> 
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