[Chimera-users] volume position/placement question

[Elaine Meng]

Hi Chen,
If you just start Chimera and open the mrc files without moving anything by hand or command, or after closing all other data, they are always in their untransformed original coordinates.  However, the zoom (scaling) might be different if you are only showing one at a time and they are not the same size, since Chimera tries to show the data at a reasonable size to fill the window.  So you would also want to make sure your window is the same size (e.g. see command "windowsize") and make the pixel size the same.  You might also want to use orthographic projection instead of perspective, which makes farther-away parts smaller, e.g. command "set projection orthographic":
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#projection>

In ChimeraX you can control pixel size with the "zoom" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html>

Chimera does not have a command to set pixel size, however. There was an experimental command "setzoom" available as a separate zip file from 2006.  Although the "window" command has been included in the standard Chimera, the "setzoom" command is not.  You could try installing that zip file but I don't know if it works with current Chimera.  For the zip file and link to details of the command and installation, search for "Set Magnification and Window Size" in this page:
<https://www.rbvi.ucsf.edu/chimera/experimental/experimental.html> 

If you had already done a roll on one volume, then close it, then open another volume, it should start out in its original position.  However, if you only hid the other volume (and did not close it) before opening the second one, the existing change in position will also be applied to the new one.  You would have to use command "reset" to put everything back to original positions.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.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 Feb 22, 2021, at 9:14 PM, Chen Mu <cm14x at my.fsu.edu> wrote:
> 
> Hi Dear List,
> I am new to Chimera and I have a question using the volume viewer:
> I have three volumes (reconstructions from different tomographic reconstruction algorithms) to compare. They are in the same size and structure as saved in the .mrc files. I will rotate one volume and adjust the volume viewer and view it. And I then will create an animation video by adding 'roll' in timeline. But the question is, how can I make sure that when I open the other volumes, all of them are in the same starting position/placement, in order to compare and each frame in the animation video to make it possible to compare, because they should start at exactly the same volume position/placement. How can I set up this placement of the volumes to be the same?
> 
> Thanks very much in advance!
> Best,
> Chen