[Chimera-users] biomt transform

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 10 13:23:43 PST 2008

On Dec 10, 2008, at 10:39 AM, Connie Oshiro wrote:
> I would like to generate the "biologically relevant" form of a  
> protein, based upon the pdb BIOMT record and am having some  
> problems.  I'm running chimera alpha version 1 build 2566 2008/10/16  
> on win32
> I tried 2 different methods, with different results:
> using pdb file 1LT8
> on the command line:
> select #0
> sym #0 #0
> GUI:
> Tools -> Higher Order Structure -> Multiscale Models...Select chains  
> "All"....Under Multimer:  Biological oligomer, click on "Make Models"
> In the first case, coordinates were displayed.  I'm guessing they  
> are correct, or at least the correct number of structures were  
> generated.
> In the second caes, I got a kind of a surface in the same area in  
> space, but not the "usual" ms (msms) surface, with no coordinates.
> Questions:
> - Are the commands I used on the command line correct?
> - If I want to use the GUI, what am I doing wrong?
> thanks, connie

Hi Connie,
You did everything right.  Both "sym" and Multiscale Models can use  
BIOMT to generate the corresponding multimer.  The "select #0" command  
is not necessary, but it doesn't cause a problem.

By default, Multiscale Models makes the extra copies as low-res  
surfaces for efficiency since you might be generating a colossal  
multimer (with zillions of atoms).   To force loading full atomic  
coordinates of all of the copies, use the Multiscale Models dialog to  
select "All" chains, then change the style (representation) to  
anything other than surface.  Once the chains are selected, you can  
use either the Multiscale Models dialog or the Actions menu to hide  
the surface and show ribbons or some atomic representation.


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

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