[Chimera-users] Measure symmetry helix

[Mariam Shirdel]

Hi!
You understood me perfectly, that is exactly what I wanted to do! Thank you
so very much!

Best regards,
Mariam


On 11 December 2012 21:14, Tom Goddard <goddard at sonic.net> wrote:

> 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.
>
>     Tom
>
>
>
>  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
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20121212/145dd735/attachment.html>