[Chimera-users] Convert the structure

[Elaine Meng]

Hi Abeer,
The short answer is yes, but I am not sure if you are asking how to  
move the structure, or how to save transformed coordinates. I will  
assume you are talking about atomic coordinates.

Certainly there are several ways to move the structure:  with the  
mouse, or by matching or docking to another structure, or by  
specifying a rotation or translation in a command.  The "turn" command  
allows rotating a specified number of degrees about a specified axis  
and center, allowing a more exact rotation than you can do by hand.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

You can save the positions of all the models with the "savepos"  
command and get them back with the "reset" command, and these  
positions will be remembered if you save a Chimera session file.    
That is one way to save your positioning work.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html#sesdef>

If you will be using any of the commands mentioned above, I recommend  
using a daily build (version 1.4) of Chimera, since these commands  
have been improved since the 1.3 release.

Another way to save your positioning work is to write out a new PDB  
file with the transformed coordinates, using File... Save PDB or the  
command "write".  There are options to use the total transformation or  
just the transformation "relative to" another model (useful if you  
have docked or matched to that other model).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.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
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Jul 29, 2009, at 2:48 AM, Abeer Shokeer wrote:

> Hello
> I would like to convert the model structure that I have prepared 90
> degree or in different position. Can I do that with Chimera?
>
> Thanks
> Abeer