[Chimera-users] rotation centers

Tom Goddard goddard at sonic.net
Tue Jan 25 18:36:36 PST 2011

Hi Ben,

   The "independent" center of rotation mode is not able to do what you 
want without great difficulty.  It can only rotate each model about its 
own geometric center with no provision to specify the center (it is 

   But it is not too hard to get what you want.  You use the "turn" 
command once for each pdb/map pair.  Suppose the first PDB is model #0 
and its map is model #1.  Use the following command

     turn z 3 120  center #1 models #0,1 coord #1

to rotate both about the z axis of the map coordinate system in 3 degree 
steps for 120 steps about the geometric center of the map.  If the next 
PDB/map pair is #2,#3 use the analogous command to rotate those.  When 
you put those two commands in a script to record a movie the first 
command completes immediately (it doesn't wait for the 120 frames) and 
so the second rotation will start at the same time (actually one frame 
later, but that shouldn't be observable at 25 frames/sec).  Put the 
commands on the same line separated by a semi-colon if you want them to 
strictly start exactly in sync (no 1 frame error).

Turn command documentation:



> Hi,
> I have a set of density maps and PDB models. I have displayed the maps
> side by side. Each map has a pdb model docked in it. I would like to
> make a movie where each map rotates around its Z axis. Each pdb should
> rotate around the Z axis of its respective map.
> I tried:
> set independent
> roll z
> The problem is that the center of the pdb models is not the same as the
> center of their respective maps. Is there a way to group one pdb with
> one map so that they rotate around the same center? Or is it possible to
> set the center of rotation of a PDB to the same value as the center of
> rotation of the map?
> Thanks in advance
> Ben

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