[Chimera-users] sym command in Chimera

Thomas Goddard goddard at cgl.ucsf.edu
Thu Aug 16 11:08:04 PDT 2007

Hi Nevin,

   The sym command places molecule copies relative to the coordinate 
frame of a density map.  If you do not have a density map open it will 
not work.  The solution is to open a density map, any map will do even 
if it is not related to your system -- it is just providing a coordinate 

   Here's a density map (potassium ion channel electron microscope data) 
if you don't have one.


You'll need to uncompress it (for example, with gunzip, or on the Mac it 
will offer to uncompress automatically when you download it) before 
opening it in Chimera.  Once it is open in Chimera and you use the sym 
command you can undisplay it with Favorites / Model Panel.  You also use 
Model Panel to freeze the map (uncheck the "active" button) in order to 
make motions of the molecule generate new positions for the molecule copies.

   Here is why a map is needed to define a coordinate frame.  You might 
think the positioning matrices could just be applied in the global 
coordinate frame.  But when you rotate the Chimera models with the mouse 
to get a different view point, that moves all the models around in the 
global frame, and that would cause all the monomers to assume a new 
arrangement if the matrices were applied to the rotated reference model. 
  So in order to be able to see you models from different view points 
without changing their relative positions the symmetries are applied 
relative to the coordinate frame of a density map.  (Could be relative 
to any other model but the command was created for people fitting 
molecules into density maps.)  If you rotate the density map and 
molecules together then the matrices still keep the same relative 
positions of the molecules.


Z. Nevin Gerek wrote:
> Hello,
> I am having another problem with sym command.  When I test on some 
> proteins including the example (1i84) provided in the website, I get
> 'No opened volume or reference model specified" error.
> I used sym and then sym #0 but they give same error. Do I need to copy 
> another feature for this command? Is there anyway I can fox this problem?
> Thanks again,
> Z. Nevin Gerek, Ph.D.
> Postdoctoral Fellow
> -----------------------------------------------------
> The Center for Biological Physics
> Arizona State University
> PO Box 871504
> Tempe, AZ 85287-1504
> Phone: (480) 727-8897
> nevin.gerek at asu.edu <mailto:nevin.gerek at asu.edu> 

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