[Chimera-users] Model translation

[Elaine Meng]

Hi David,
See the "move" command.  It has been improved since the production  
release 1.3, so I recommend using a daily build (1.4).  Here is the  
documentation for its current incarnation.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

Since you can only bond things in the same model, it sounds like you  
would first do all the positioning with "move" and then use  
"combine" (or "copy/combine" in the Model Panel) to merge them into a  
single model, and then add bonds.  Note that when you combine models  
it will make you either change chain IDs or renumber residues to  
avoid conflicts where multiple residues shave the same number/chain  
identifier.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>

Hmm, a nanotube may be even trickier.  If it is already just one big  
residue, I'm not sure what will happen... it *might* work...

I guess it depends what you are going to do with the structure.  You  
could make "pseudobonds" (see PseudoBond Reader tool) between the  
different models instead of bothering to combine them into a single  
model.  Another possibility is to write the multiple models out in  
their new coordinates as multiple models and then do your own text- 
editing to make them a single model, and read them back in.  You  
would still want to avoid conflicts where multiple residues or  
multiple atoms have the same identifiers, however.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
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 8, 2009, at 9:09 AM, David Chenoweth wrote:

> Hi,
> Can anyone tell me the easiest way to translate an entire model by a
> defined amount (angstroms) in a defined direction. I have a slice of a
> nanotube and I would like to open it several times, translate each
> section, and make bonds between the translated sections in order to
> create a longer nanotube and then save the new coordinates as a new
> model.
> Thanks,
> Dave
>