[Chimera-users] Question about disulfide bonds and energy minimization

[Elaine Meng]

Hi Steve,
As discussed in this very recent post, you can certainly move structures indepedently of one another, with the mouse or with commands:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-July/014825.html>

Also as mentioned in the post, for side-by-side comparisons I first superimpose the structures, rotate everything to the desired view, and then translate the structures apart with the “move” command without changing their orientations.

There are several ways to superimpose structures.  Probably easiest for your situation is Matchmaker (in Tools… Structure Comparison).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

You should probably save positions so that they are easily restored, and then save the session.  For saving/restoring positions, see “savepos” and “reset”  commands. 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>

Another thing to consider for side-by-side comparisons is to use orthographic projection (“set projection orthographic”) to avoid distortion from the default perspective projection (“set projection perspective” to turn it back on):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#projection>

See also this image tutorial for a detailed example with side-by-side comparisons and saved positions:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 23, 2018, at 6:06 AM, Steven Douglas Aird <steven.aird at oist.jp> wrote:
> 
> Dear Elaine and Eric,
> 
> As always, thank you for your thorough explanations.  Everything made sense and I had no trouble accomplishing my objective by following your instructions.
> 
> Now I have created two homologous structures, one from humans and the other from snakes, and I would like to display them side by side in the same orientation so that the structural similarities and differences are self-evident.  However, when I open the second structure, it always opens on top of the first structure, and two random coils (one from each structure) are actually intertwined.  Eventually I discovered that if I select Tools > Structure Comparison > Tile Structures, I can separate them.  I thought that the two would appear as two chains in the Chimera window, but in fact, they appear in a list of two items under Chain A, i.e., the same chain, which probably explains why one cannot be moved without the other.
> 
> Is there a way to designate them as separate chains?  Would that enable me to move one without the other?
> 
> I apologize for asking such basic questions, but thank you again for your help!
> 
> Sincerely yours,
> 
> Steve Aird