[Chimera-users] Helix voxels labeling

Tom Goddard goddard at sonic.net
Tue Aug 22 11:06:51 PDT 2017

Hi Natan,

  You can use the molmap and mask commands to get a binary mask around helices, for example,

open 3p2i
molmap helix 10 grid 2 model #1
vol #1 level 0.25
mask ones #1
volume #1 hide
volume #2 save helixmask.mrc

These commands open PDB file 3p2i, create a density map at resolution 10 Angstroms with grid spacing 2 Angstroms for the helix atoms calling the resulting map #1, set the surface contour level of that helix map to 0.25, create a 0/1 binary mask with one values within the surface of the helix map, hide the original helix map so you can see the binary mask, and save the binary mask to an MRC file.  All the commands are described in great detail in the documentation.


> On Aug 22, 2017, at 4:42 AM, natan geier  wrote:
> Hello,
> I am currently studying the connection between density maps and the secondary structure elements.
> I have a density map file for a certain protein, giving for each voxel a density value, and what I am missing is a "helix map", giving a binary value for each voxel, representing wether it is a part of a helix or not.
> In order to build this "helix map", I need to use the .pdb file of that protein, but I am not really sure how to extract an appropriate 3D boolean matrix out of this file.
> Any suggestions would be greatly appreciated.
> Thanks
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