[chimerax-users] Identifying symmetry of a model

[Y. Mutum]

Hi Elaine

I was thinking of a follow-up on this question, as this question is linked to the previous one.

This answer might be slightly subjective, but given your ChimeraX expertise in visual representation, your thoughts would nonetheless be helpful.

So, now that we have aligned the rotation axis perpendicular to the screen (from the previous question), I am thinking of putting in a small scalebar - say, 50 A. I created this rectange object (command: shape rectange width 50 height 2), along with the rotation axis and the other 3cx5.pdb's in ChimeraX(the email below)

  1.  Where would you recommend placing the scale bar (in this case, a rectange) wrt the model 3cx5, considering we want a view perpendicular the rotation axis, (showing the whole protein-complex to get a genral ide of the size of the object)?  (considering that a distance is defined for in a plane).
  2.  The other related question is - if suppose, we draw a line b/w the Fe-centres of the hemes (by distance command from #1/C:4002 and #2/C:4002), how do we align the rectange object against this distance line. I can think of doing aligning it manually, but this might not be entirely accurate and I am not sure if there's some other method - such as aligning this rectange perpendicular to the rotation-axis line (generated from the previous email).


I am also open to consider other alternatives, rather than this method as well.

Thanks
Yaikhomba
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 18 January 2021 18:09
To: Y. Mutum <ym337 at cam.ac.uk>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Identifying symmetry of a model

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210205/5c7e362d/attachment-0001.html>