[Chimera-users] volume eraser and imod isosurface

Tom Goddard goddard at sonic.net
Wed Jan 6 11:14:42 PST 2016


Hi Wouter,

  To add some more info to what Elaine said, there are two kinds of IMOD files read by Chimera, density maps which often have file suffix *.rec (for reconstruction) or *.mrc, and segmentation files with suffix *.mod.  The segmentation files just contain surfaces, not the density map data.  Since Volume Eraser erases density values and doesn’t do anything with surfaces it doesn’t work with the *.mod files.  There isn’t a tool for erasing parts of surfaces in Chimera.  You found “Hide Dust” that can hide the small connected surface blobs.  It is also possible to by hand hide other connected surface blobs with the “sop split” command to make a copy of the surface where each blob is selectable, then select any blobs and use menu Actions / Surface / Hide to undisplay those.  One last trick, the Chimera Surface Zone tool or “sop zone” command can display just the parts of a surface within some distance of a set of markers, and the Color Zone tool could color surfaces to be completely transparent within a zone around markers, and the Volume Tracer tool can place markers.  So that is another route to hide certain parts of a surface.

	Tom


> On Jan 6, 2016, at 9:07 AM, Elaine Meng  wrote:
> 
> Dear Wouter,
> The issue is that an IMOD file makes surfaces in Chimera, not a volume model (map or density grid with associated values at each grid point).
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object>
> 
> Volume Eraser only works with volume models, formats listed here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>
> 
> Maybe your original data was or could be written in one of those formats?
> 
> Also, Hide Dust only hides small surface bits; it does not delete any data.
> 
> I hope this makes it clearer,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> P.S. appears to be a duplicate question, I’ll just answer this one
> 
> On Jan 6, 2016, at 6:39 AM, Wouter Van Putte wrote:
> 
>> Dear,
>> 
>> I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed?
>> 
>> best wishes,
>> 
>> Wouter
> 
> 
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