[Chimera-users] Color blobs automatically

Tom Goddard goddard at sonic.net
Mon Oct 19 10:52:03 PDT 2015


Hi Petr,

  How about you make a PDB file that contains an atom at each lattice position using whatever scripting language you like to use.  Open that PDB in Chimera, make sure the atoms overlap the density map blobs, then use the Color Zone tool (menu Tools / Volume Data / Color Zone) to color the density near those atoms to match the atoms.  Color zone colors a surface within a specified distance range of some selected atoms to match the colors of those atoms.

	Tom


> On Oct 19, 2015, at 2:07 AM, wrote:
> 
> Hello,
> 
> I have both periodically distributed blobs and blobs, which are randomly distributed in my volume data. I know the translational vectors of the periodic net of blobs and I would like to automatically color them to distinguish them from the rest of the blobs. Is there a way to tell Chimera to color the blobs, which contain voxel with particular x, y, z coordinates? Or is there some other way to do this job?
> 
> Best regards,
> 
> Petr
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