[Chimera-users] Measure symmetry helix
goddard at sonic.net
Tue Dec 11 12:14:59 PST 2012
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.
> 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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