[chimera-dev] Rotation of a single submolecule in a mol2

Elaine Meng meng at cgl.ucsf.edu
Sat Aug 8 11:56:26 PDT 2009

Hi Chris,
In version 1.4, the movement commands (move, turn, rock, roll) allow  
specifying which models should move, and you don't have to mess with  
activation/deactivation.  For example:

turn x 90 models #0.1

In the production release 1.3, these commands are less powerful and  
do not have the models option.  I can't think of any command-line  
approach in 1.3, since as far as I can tell the "select" command for  
model activation does not work on submodels, and the only way to  
differentially activate submodels of the same model is to use the  
Model Panel.

We are planning to make a snapshot release in the next couple of  
weeks, however, so there should soon be something besides daily  
builds with these and the many other new capabilities, listed here:

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

On Aug 8, 2009, at 8:48 AM, christopher lau wrote:

> Hi,
> I am currently working on a project to modify the ViewDock program  
> to work on a Tiled Wall Display.  I am reluctant to require the  
> user to download the daily build to allow use of molecule specific  
> rotations in my TDW ViewDock program.  I was wondering if there was  
> a way from the Command Line to rotate a single molecule, say #0.1,  
> without rotating all the molecules in model #0.  If it is possible  
> to inactivate all the submodels except for #0.1, I can use the  
> rotation commands (roll, rock, turn) to rotate a single  
> submolecule. I know that I can split the submolecules into  
> individual molecules and apply the rotations in this manner, but  
> that would make the data handling very difficult.  I was having  
> problems learning how to deactivate models using the select command  
> with the current stable version of chimera.  I was wondering if  
> anyone had any insight on this problem.  I would prefer to not  
> require the daily build and would not want to use the split command  
> line command to separate the submolecules into separate molecules  
> for rotation.
> Thanks for your help,
> Chris
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