Generate a helical density map of desired length from a reconstruction

Helical Processing
#1
  1. I recently completely a helical reconstruction with resolution up to 3.6Å. Now I want to generate the whole 3.6Å map to a much larger length (it is a phage tail density map). I will need the asymmetric map (at 3.6Å) so that I can symmetrize it to generate a 1200Å long map (the map is ~256Å long). How to obtain the asymmetric map ?

Is there any alternate way to do it ?

#2

You can use the symmetry commands in Chimera(X).

#3

@Daniel,
How can it be done in Chimera(X)- what will be the command ?
Does it need the asymmetric unit or a density map of any length will do .
Waiting to hear from you.

#4

The commands are sym, vol symmetry, and some others. Look them up in the ChimeraX documentation.

#5

It will be good the have the whole command (if you have). If not, I will then like to hear from the cryosparc group.

Thanks.

#6

Hi @Andy,

Apologies for the delayed reply. The Chimera documentation is quite complete on the sym command, which generates symmetry copies of an atomic model. The command usage is shown in the docs, and for helical symmetry in particular, the sym-type would be specified using H,rise,angle,n[,offset]. The “axis” that should be used is the z-axis of the volume, perpendicular to the xy plane. The “center” should be located at the center of the box, i.e., x, y, and z coordinates of N/2. If you aren’t sure about the symmetry, you can use the Chimera measure symmetry command.

Best,
Michael

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