[Chimera-users] symmetry axis

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 8 10:04:30 PST 2016


Hi Jiri,
The axis from “measure rotation” is a marker model or fake molecule model made of two “atoms" with a “bond" between them.  You can adjust it the same ways as you would change the display of sticks in a model.

One way is to select the axis (fake bond) with Ctrl-click, then open Selection Inspector such as by clicking the green magnifying glass in the bottom right corner of the Chimera window.  In that dialog, under Inspect: Bond, you can change “color” by clicking the square color well to show the Color Editor and using it to specify a color, and you can change “radius” stick thickness by entering a different value, and set “displayed” to “true” instead of “if atoms shown” because you may want to hide the end atoms if they are now a different radius than the axis between them.  

To hide the atoms, you would need to know the model number of the axis, which you can figure out by looking at the Model Panel (under Favorites menu) and then enter a command with that model number, for example:

~disp #2@*

… which means undisplay all atoms in model 2.

To move and rotate that axis model you could use “move” and “turn” commands.  See the command options with commands “help move” and “help turn”.

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 Dec 8, 2016, at 9:43 AM, chemocev marker <jirivitali at gmail.com> wrote:
> 
> Dear Dr. Elaine
> Thanks for your help. I am able to draw the symmetry axis, and can you let me know how can I change the representation of the drawn vector, its color and diameter. and If  I make another copy of the same vector how can I move the second vector to a particular axis a by given rotation angle.
> Sincerely
> Jiri
> 
> On Mon, Nov 21, 2016 at 6:48 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Jiri,
> As I understand it, you would need to open two separate copies of the structure, superimpose the two sets of atoms for which you want to see the axis (like A to B, or domain 1 of A to domain 2 of A), and then use command “measure rotation”.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>
> 
> There are various different ways to superimpose sets of atoms as discussed here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> 
> 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 Nov 20, 2016, at 2:30 PM, chemocev marker <jirivitali at gmail.com> wrote:
> >
> > Hi All
> > I am interested to measure the symmetry axis of individual sub-unit (chain A & chain B) along with the symmetry axis of the heterodimer (AB). Each chain has 2 domains and 2 fold rotations axis, and I can measure by removing 1 chain and measure for the other. Is there way to measure the inter-domain symmetry axis of the heterodimer molecule.
> > best
> > Jiri




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