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
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
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@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
participants (2)
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Mariam Shirdel -
Tom Goddard