[Chimera-users] Measure symmetry helix

Tom Goddard goddard at sonic.net
Tue Dec 11 12:14:59 PST 2012

Hi Mariam,

   If I understand it, you have a 5-start helix but you just want to 
place molecule copies for one of the 5 helical strands instead of for 
all 5.  How about

   volume #0 originIndex 39,39,38 symmetry h,8.97,-111.86,10
   sym #1 group #0

The sym command you tried is close, just drop the "c5*", add a ",10" for 
10 subunits along the helix, and make sure your map origin index is 39 
39 38 (either with the volume dialog Coordinates panel or volume 
command).  The z index doesn't need to be 38, can be anything since the 
helix axis is z.


> Hi!
> I'm trying to measure the symmetry of an EM density map to fit a pdb 
> to it and make several copies. When I run the commands in the command 
> line:  me sym #0 min 0.89 helix 8.97,-111.86, the result I get is 
> Symmetry EMnew.spi: Helix C5, rise 8.97, angle -111.9, center 39 39 
> 38, n 30.
> The problem is that when I run sym #1 group #0 update true, I get a 
> pentagon base which goes through the whole helix. I just want the 
> measure symmetry to give me Helix, without the C5. What are the 
> commands to achieve this? I tried: sym #1 group c5*h,8.97,-111.86, but 
> it didn't work, and I don't think that's the correct way for me to do it.
> Does anyone know what to do?
> Best regards,
> Mariam Shirdel

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